begin restoring Sqlite functionality. (#11)

CONTRIBUTING.md

@@ -13,7 +13,6 @@ Fasten is made up of a handful of different components. Here's a summary of the
 
 **Backend**
 - Go `v1.18.3`
-- CouchDB `v3.2`
 
 **Misc**
 - Docker `v20.10.17`
@@ -65,6 +64,8 @@ web:
   src:
     frontend:
       path: ./dist
+database:
+  location: 'fasten.db'
 log:
   file: '' #absolute or relative paths allowed, eg. web.log
   level: INFO
@@ -79,10 +80,6 @@ cd frontend
 npm run dist -- -c sandbox
 
 # In terminal #2, run the following
-docker build -t fasten-couchdb -f docker/couchdb/Dockerfile .
-docker run --rm -it -p 5984:5984 -v `pwd`/.couchdb/data:/opt/couchdb/data -v `pwd`/.couchdb/config:/opt/couchdb/etc/local.d fasten-couchdb
-
-# In terminal #3, run the following
 go mod vendor
 go run backend/cmd/fasten/fasten.go start --config ./config.dev.yaml --debug
 
@@ -95,13 +92,8 @@ Now you can open a browser to `http://localhost:9090` to see the Fasten UI.
 The following URL's and credentials may be helpful as you're developing
 
 - http://localhost:9090/web/dashboard - WebUI
-- http://localhost:9090/database - CouchDB API proxy
-- http://localhost:5984/_utils/ - CouchDB admin UI
 
 ### Credentials
-- Couchdb:
-  - username: `admin`
-  - password: `mysecretpassword`
 - WebUI: 
   - username: `testuser`
   - password: `testuser`

TODO.md

@@ -0,0 +1,5 @@
+
+- [x] pagination
+- [x] references/links
+- [x] manual sync
+- fix sources where refresh token is missing (panics)

backend/pkg/auth/jwt_utils.go

@@ -0,0 +1,60 @@
+package auth
+
+import (
+	"errors"
+	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
+	"github.com/golang-jwt/jwt/v4"
+	"log"
+	"time"
+)
+
+func JwtGenerateFastenTokenFromUser(user models.User, issuerSigningKey string) (string, error) {
+	log.Printf("ISSUER KEY: " + issuerSigningKey)
+	userClaims := UserRegisteredClaims{
+		FullName: user.FullName,
+		UserId:   user.ID.String(),
+		RegisteredClaims: jwt.RegisteredClaims{
+			// In JWT, the expiry time is expressed as unix milliseconds
+			ExpiresAt: jwt.NewNumericDate(time.Now().Add(1 * time.Hour)),
+			IssuedAt:  jwt.NewNumericDate(time.Now()),
+			Issuer:    "docker-fastenhealth",
+			Subject:   user.Username,
+		},
+	}
+
+	//FASTEN_JWT_ISSUER_KEY
+	token := jwt.NewWithClaims(jwt.SigningMethodHS256, userClaims)
+	//token.Header["kid"] = "docker"
+	tokenString, err := token.SignedString([]byte(issuerSigningKey))
+
+	if err != nil {
+		return "", err
+	}
+	return tokenString, nil
+}
+
+func JwtValidateFastenToken(encryptionKey string, signedToken string) (*UserRegisteredClaims, error) {
+	token, err := jwt.ParseWithClaims(
+		signedToken,
+		&UserRegisteredClaims{},
+		func(token *jwt.Token) (interface{}, error) {
+			if jwt.SigningMethodHS256 != token.Method {
+				return nil, errors.New("Invalid signing algorithm")
+			}
+			return []byte(encryptionKey), nil
+		},
+	)
+	if err != nil {
+		return nil, err
+	}
+	claims, ok := token.Claims.(*UserRegisteredClaims)
+	if !ok {
+		err = errors.New("couldn't parse claims")
+		return nil, err
+	}
+	if claims.ExpiresAt.Unix() < time.Now().Local().Unix() {
+		err = errors.New("token expired")
+		return nil, err
+	}
+	return claims, nil
+}

backend/pkg/auth/user_registered_claims.go

@@ -0,0 +1,9 @@
+package auth
+
+import "github.com/golang-jwt/jwt/v4"
+
+type UserRegisteredClaims struct {
+	FullName string `json:"full_name"`
+	UserId   string `json:"user_id"`
+	jwt.RegisteredClaims
+}

backend/pkg/config/config.go

@@ -26,11 +26,7 @@ func (c *configuration) Init() error {
 	c.SetDefault("web.listen.basepath", "")
 	c.SetDefault("web.src.frontend.path", "/opt/fasten/web")
 
-	c.SetDefault("couchdb.scheme", "http")
-	c.SetDefault("couchdb.host", "localhost")
-	c.SetDefault("couchdb.port", "5984")
-	c.SetDefault("couchdb.admin.username", "admin")
-	c.SetDefault("couchdb.admin.password", "mysecretpassword")
+	c.SetDefault("database.location", "/opt/fasten/db/fasten.db") //TODO: should be /opt/fasten/fasten.db
 
 	c.SetDefault("jwt.issuer.key", "thisismysupersecuressessionsecretlength")
 

backend/pkg/database/couchdb_repository.go

@@ -1,122 +0,0 @@
-package database
-
-import (
-	"context"
-	"fmt"
-	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
-	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
-	"github.com/go-kivik/couchdb/v3"
-	_ "github.com/go-kivik/couchdb/v3" // The CouchDB driver
-	"github.com/go-kivik/kivik/v3"
-	"github.com/sirupsen/logrus"
-	"log"
-)
-
-func NewRepository(appConfig config.Interface, globalLogger logrus.FieldLogger) (DatabaseRepository, error) {
-	////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-	// Couchdb setup
-	////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-	couchdbUrl := fmt.Sprintf("%s://%s:%s", appConfig.GetString("couchdb.scheme"), appConfig.GetString("couchdb.host"), appConfig.GetString("couchdb.port"))
-
-	globalLogger.Infof("Trying to connect to couchdb: %s\n", couchdbUrl)
-
-	database, err := kivik.New("couch", couchdbUrl)
-	if err != nil {
-		return nil, fmt.Errorf("Failed to connect to database! - %v", err)
-	}
-
-	err = database.Authenticate(context.Background(),
-		couchdb.BasicAuth(
-			appConfig.GetString("couchdb.admin.username"),
-			appConfig.GetString("couchdb.admin.password")),
-	)
-
-	if err != nil {
-		return nil, fmt.Errorf("Failed to authenticate to database! - %v", err)
-	}
-	globalLogger.Infof("Successfully connected to couchdb: %s\n", couchdbUrl)
-
-	deviceRepo := couchdbRepository{
-		appConfig: appConfig,
-		logger:    globalLogger,
-		client:    database,
-	}
-	return &deviceRepo, nil
-}
-
-type couchdbRepository struct {
-	appConfig config.Interface
-	logger    logrus.FieldLogger
-
-	client *kivik.Client
-}
-
-type couchDbUser struct {
-	ID       string   `json:"_id"`
-	Name     string   `json:"name"`
-	Type     string   `json:"type"`
-	Roles    []string `json:"roles"`
-	Password string   `json:"password"`
-
-	FullName string `json:"full_name"`
-}
-
-func (cr *couchdbRepository) CreateUser(ctx context.Context, user *models.User) error {
-
-	newUser := &couchDbUser{
-		ID:       fmt.Sprintf("%s%s", kivik.UserPrefix, user.Username),
-		Name:     user.Username,
-		Type:     "user",
-		Roles:    []string{},
-		Password: user.Password,
-
-		FullName: user.FullName,
-	}
-	db := cr.client.DB(ctx, "_users")
-	_, err := db.Put(ctx, newUser.ID, newUser)
-	if err != nil {
-		return err
-	}
-
-	//TODO: we should create an index for this database now
-	//db.CreateIndex(ctx, )
-	return err
-}
-
-func (cr *couchdbRepository) VerifyUser(ctx context.Context, user *models.User) error {
-
-	couchdbUrl := fmt.Sprintf("%s://%s:%s", cr.appConfig.GetString("couchdb.scheme"), cr.appConfig.GetString("couchdb.host"), cr.appConfig.GetString("couchdb.port"))
-
-	userDatabase, err := kivik.New("couch", couchdbUrl)
-	if err != nil {
-		return fmt.Errorf("Failed to connect to database! - %v", err)
-	}
-
-	err = userDatabase.Authenticate(context.Background(),
-		couchdb.BasicAuth(user.Username, user.Password),
-	)
-	session, err := userDatabase.Session(context.Background())
-	if err != nil {
-		return err
-	}
-	log.Printf("SESSION INFO: %v", session)
-	//TODO: return session info
-
-	//lookup the user in the user database using admin creds
-	adminDb := cr.client.DB(ctx, "_users")
-	userRow := adminDb.Get(ctx, kivik.UserPrefix+session.Name)
-	userDoc := map[string]interface{}{}
-	err = userRow.ScanDoc(&userDoc)
-	if err != nil {
-		return err
-	}
-
-	if userFullName, hasUserFullName := userDoc["full_name"]; hasUserFullName {
-		user.FullName = userFullName.(string)
-	}
-	return nil
-}
-
-func (cr *couchdbRepository) Close() error {
-	return nil
-}

backend/pkg/database/interface.go

@@ -2,6 +2,7 @@ package database
 
 import (
 	"context"
+	sourcePkg "github.com/fastenhealth/fasten-sources/clients/models"
 	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
 )
 
@@ -10,5 +11,24 @@ type DatabaseRepository interface {
 	Close() error
 
 	CreateUser(context.Context, *models.User) error
-	VerifyUser(context.Context, *models.User) error
+
+	GetUserByEmail(context.Context, string) (*models.User, error)
+	GetCurrentUser(context.Context) *models.User
+
+	GetSummary(ctx context.Context) (*models.Summary, error)
+
+	GetResourceBySourceType(context.Context, string, string) (*models.ResourceFhir, error)
+	GetResourceBySourceId(context.Context, string, string) (*models.ResourceFhir, error)
+	ListResources(context.Context, models.ListResourceQueryOptions) ([]models.ResourceFhir, error)
+	GetPatientForSources(ctx context.Context) ([]models.ResourceFhir, error)
+	//UpsertProfile(context.Context, *models.Profile) error
+	//UpsertOrganziation(context.Context, *models.Organization) error
+
+	CreateSource(context.Context, *models.SourceCredential) error
+	GetSource(context.Context, string) (*models.SourceCredential, error)
+	GetSourceSummary(context.Context, string) (*models.SourceSummary, error)
+	GetSources(context.Context) ([]models.SourceCredential, error)
+
+	//used by Client
+	UpsertRawResource(ctx context.Context, sourceCredentials sourcePkg.SourceCredential, rawResource sourcePkg.RawResourceFhir) (bool, error)
 }

backend/pkg/database/mock/mock_database.go

@@ -1,5 +1,5 @@
 // Code generated by MockGen. DO NOT EDIT.
-// Source: interface.go
+// SourceCredential: interface.go
 
 // Package mock_database is a generated GoMock package.
 package mock_database

backend/pkg/database/sqlite_repository.go

@@ -0,0 +1,442 @@
+package database
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+	sourceModel "github.com/fastenhealth/fasten-sources/clients/models"
+	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
+	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
+	"github.com/gin-gonic/gin"
+	"github.com/glebarez/sqlite"
+	"github.com/google/uuid"
+	"github.com/sirupsen/logrus"
+	"gorm.io/datatypes"
+	"gorm.io/gorm"
+	"net/url"
+	"strings"
+)
+
+func NewRepository(appConfig config.Interface, globalLogger logrus.FieldLogger) (DatabaseRepository, error) {
+	//backgroundContext := context.Background()
+
+	////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+	// Gorm/SQLite setup
+	////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+	globalLogger.Infof("Trying to connect to sqlite db: %s\n", appConfig.GetString("database.location"))
+
+	// When a transaction cannot lock the database, because it is already locked by another one,
+	// SQLite by default throws an error: database is locked. This behavior is usually not appropriate when
+	// concurrent access is needed, typically when multiple processes write to the same database.
+	// PRAGMA busy_timeout lets you set a timeout or a handler for these events. When setting a timeout,
+	// SQLite will try the transaction multiple times within this timeout.
+	// fixes #341
+	// https://rsqlite.r-dbi.org/reference/sqlitesetbusyhandler
+	// retrying for 30000 milliseconds, 30seconds - this would be unreasonable for a distributed multi-tenant application,
+	// but should be fine for local usage.
+	pragmaStr := sqlitePragmaString(map[string]string{
+		"busy_timeout": "30000",
+		"foreign_keys": "ON",
+	})
+	database, err := gorm.Open(sqlite.Open(appConfig.GetString("database.location")+pragmaStr), &gorm.Config{
+		//TODO: figure out how to log database queries again.
+		//Logger: logger
+		DisableForeignKeyConstraintWhenMigrating: true,
+	})
+
+	if strings.ToUpper(appConfig.GetString("log.level")) == "DEBUG" {
+		database = database.Debug() //set debug globally
+	}
+
+	if err != nil {
+		return nil, fmt.Errorf("Failed to connect to database! - %v", err)
+	}
+	globalLogger.Infof("Successfully connected to fasten sqlite db: %s\n", appConfig.GetString("database.location"))
+
+	//TODO: automigrate for now
+	err = database.AutoMigrate(
+		&models.User{},
+		&models.SourceCredential{},
+		&models.ResourceFhir{},
+	)
+	if err != nil {
+		return nil, fmt.Errorf("Failed to automigrate! - %v", err)
+	}
+
+	// create/update admin user
+	adminUser := models.User{}
+	err = database.FirstOrCreate(&adminUser, models.User{Username: "admin"}).Error
+	if err != nil {
+		return nil, fmt.Errorf("Failed to create admin user! - %v", err)
+	}
+
+	deviceRepo := sqliteRepository{
+		appConfig:  appConfig,
+		logger:     globalLogger,
+		gormClient: database,
+	}
+	return &deviceRepo, nil
+}
+
+type sqliteRepository struct {
+	appConfig config.Interface
+	logger    logrus.FieldLogger
+
+	gormClient *gorm.DB
+}
+
+func (sr *sqliteRepository) Close() error {
+	return nil
+}
+
+////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// User
+////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+
+func (sr *sqliteRepository) CreateUser(ctx context.Context, user *models.User) error {
+	if err := user.HashPassword(user.Password); err != nil {
+		return err
+	}
+	record := sr.gormClient.Create(user)
+	if record.Error != nil {
+		return record.Error
+	}
+	return nil
+}
+func (sr *sqliteRepository) GetUserByEmail(ctx context.Context, username string) (*models.User, error) {
+	var foundUser models.User
+	result := sr.gormClient.Where(models.User{Username: username}).First(&foundUser)
+	return &foundUser, result.Error
+}
+
+func (sr *sqliteRepository) GetCurrentUser(ctx context.Context) *models.User {
+	ginCtx := ctx.(*gin.Context)
+	var currentUser models.User
+	sr.gormClient.First(&currentUser, models.User{Username: ginCtx.MustGet("AUTH_USERNAME").(string)})
+
+	return &currentUser
+}
+
+////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// User
+////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+
+func (sr *sqliteRepository) GetSummary(ctx context.Context) (*models.Summary, error) {
+
+	// we want a count of all resources for this user by type
+	var resourceCountResults []map[string]interface{}
+
+	//group by resource type and return counts
+	// SELECT source_resource_type as resource_type, COUNT(*) as count FROM resource_fhirs WHERE source_id = "53c1e930-63af-46c9-b760-8e83cbc1abd9" GROUP BY source_resource_type;
+	result := sr.gormClient.WithContext(ctx).
+		Model(models.ResourceFhir{}).
+		Select("source_id, source_resource_type as resource_type, count(*) as count").
+		Group("source_resource_type").
+		Where(models.OriginBase{
+			UserID: sr.GetCurrentUser(ctx).ID,
+		}).
+		Scan(&resourceCountResults)
+	if result.Error != nil {
+		return nil, result.Error
+	}
+
+	// we want a list of all sources (when they were last updated)
+	sources, err := sr.GetSources(ctx)
+	if err != nil {
+		return nil, err
+	}
+
+	// we want the main Patient for each source
+	patients, err := sr.GetPatientForSources(ctx)
+	if err != nil {
+		return nil, err
+	}
+
+	if resourceCountResults == nil {
+		resourceCountResults = []map[string]interface{}{}
+	}
+	summary := &models.Summary{
+		Sources:            sources,
+		ResourceTypeCounts: resourceCountResults,
+		Patients:           patients,
+	}
+
+	return summary, nil
+}
+
+////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// Resource
+////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+
+func (sr *sqliteRepository) UpsertRawResource(ctx context.Context, sourceCredential sourceModel.SourceCredential, rawResource sourceModel.RawResourceFhir) (bool, error) {
+
+	source := sourceCredential.(models.SourceCredential)
+
+	wrappedResourceModel := &models.ResourceFhir{
+		OriginBase: models.OriginBase{
+			ModelBase:          models.ModelBase{},
+			UserID:             source.UserID,
+			SourceID:           source.ID,
+			SourceResourceID:   rawResource.SourceResourceID,
+			SourceResourceType: rawResource.SourceResourceType,
+		},
+		ResourceRaw: datatypes.JSON(rawResource.ResourceRaw),
+	}
+
+	sr.logger.Infof("insert/update (%v) %v", rawResource.SourceResourceType, rawResource.SourceResourceID)
+
+	createResult := sr.gormClient.WithContext(ctx).Where(models.OriginBase{
+		SourceID:           wrappedResourceModel.GetSourceID(),
+		SourceResourceID:   wrappedResourceModel.GetSourceResourceID(),
+		SourceResourceType: wrappedResourceModel.GetSourceResourceType(), //TODO: and UpdatedAt > old UpdatedAt
+	}).FirstOrCreate(wrappedResourceModel)
+
+	if createResult.Error != nil {
+		return false, createResult.Error
+	} else if createResult.RowsAffected == 0 {
+		//at this point, wrappedResourceModel contains the data found in the database.
+		// check if the database resource matches the new resource.
+		if wrappedResourceModel.ResourceRaw.String() != string(rawResource.ResourceRaw) {
+			updateResult := createResult.Updates(wrappedResourceModel)
+			return updateResult.RowsAffected > 0, updateResult.Error
+		} else {
+			return false, nil
+		}
+
+	} else {
+		//resource was created
+		return createResult.RowsAffected > 0, createResult.Error
+	}
+
+	//return results.RowsAffected > 0, results.Error
+
+	//if sr.gormClient.Debug().WithContext(ctx).
+	//	Where(models.OriginBase{
+	//		SourceID:           wrappedResourceModel.GetSourceID(),
+	//		SourceResourceID:   wrappedResourceModel.GetSourceResourceID(),
+	//		SourceResourceType: wrappedResourceModel.GetSourceResourceType(), //TODO: and UpdatedAt > old UpdatedAt
+	//	}).Updates(wrappedResourceModel).RowsAffected == 0 {
+	//	sr.logger.Infof("resource does not exist, creating: %s %s %s", wrappedResourceModel.GetSourceID(), wrappedResourceModel.GetSourceResourceID(), wrappedResourceModel.GetSourceResourceType())
+	//	return sr.gormClient.Debug().Create(wrappedResourceModel).Error
+	//}
+	//return nil
+}
+
+func (sr *sqliteRepository) UpsertResource(ctx context.Context, resourceModel *models.ResourceFhir) error {
+	sr.logger.Infof("insert/update (%T) %v", resourceModel, resourceModel)
+
+	if sr.gormClient.WithContext(ctx).
+		Where(models.OriginBase{
+			SourceID:           resourceModel.GetSourceID(),
+			SourceResourceID:   resourceModel.GetSourceResourceID(),
+			SourceResourceType: resourceModel.GetSourceResourceType(), //TODO: and UpdatedAt > old UpdatedAt
+		}).Updates(resourceModel).RowsAffected == 0 {
+		sr.logger.Infof("resource does not exist, creating: %s %s %s", resourceModel.GetSourceID(), resourceModel.GetSourceResourceID(), resourceModel.GetSourceResourceType())
+		return sr.gormClient.Create(resourceModel).Error
+	}
+	return nil
+}
+
+func (sr *sqliteRepository) ListResources(ctx context.Context, queryOptions models.ListResourceQueryOptions) ([]models.ResourceFhir, error) {
+
+	queryParam := models.ResourceFhir{
+		OriginBase: models.OriginBase{
+			UserID: sr.GetCurrentUser(ctx).ID,
+		},
+	}
+
+	if len(queryOptions.SourceResourceType) > 0 {
+		queryParam.OriginBase.SourceResourceType = queryOptions.SourceResourceType
+	}
+
+	if len(queryOptions.SourceID) > 0 {
+		sourceUUID, err := uuid.Parse(queryOptions.SourceID)
+		if err != nil {
+			return nil, err
+		}
+
+		queryParam.OriginBase.SourceID = sourceUUID
+	}
+
+	manifestJson, _ := json.MarshalIndent(queryParam, "", "  ")
+	sr.logger.Infof("THE QUERY OBJECT===========> %v", string(manifestJson))
+
+	var wrappedResourceModels []models.ResourceFhir
+	results := sr.gormClient.WithContext(ctx).
+		Where(queryParam).
+		Find(&wrappedResourceModels)
+
+	return wrappedResourceModels, results.Error
+}
+
+func (sr *sqliteRepository) GetResourceBySourceType(ctx context.Context, sourceResourceType string, sourceResourceId string) (*models.ResourceFhir, error) {
+	queryParam := models.ResourceFhir{
+		OriginBase: models.OriginBase{
+			UserID:             sr.GetCurrentUser(ctx).ID,
+			SourceResourceType: sourceResourceType,
+			SourceResourceID:   sourceResourceId,
+		},
+	}
+
+	var wrappedResourceModel models.ResourceFhir
+	results := sr.gormClient.WithContext(ctx).
+		Where(queryParam).
+		First(&wrappedResourceModel)
+
+	return &wrappedResourceModel, results.Error
+}
+
+func (sr *sqliteRepository) GetResourceBySourceId(ctx context.Context, sourceId string, sourceResourceId string) (*models.ResourceFhir, error) {
+	sourceIdUUID, err := uuid.Parse(sourceId)
+	if err != nil {
+		return nil, err
+	}
+
+	queryParam := models.ResourceFhir{
+		OriginBase: models.OriginBase{
+			UserID:           sr.GetCurrentUser(ctx).ID,
+			SourceID:         sourceIdUUID,
+			SourceResourceID: sourceResourceId,
+		},
+	}
+
+	var wrappedResourceModel models.ResourceFhir
+	results := sr.gormClient.WithContext(ctx).
+		Where(queryParam).
+		First(&wrappedResourceModel)
+
+	return &wrappedResourceModel, results.Error
+}
+
+// Get the patient for each source (for the current user)
+func (sr *sqliteRepository) GetPatientForSources(ctx context.Context) ([]models.ResourceFhir, error) {
+
+	//SELECT * FROM resource_fhirs WHERE user_id = "" and source_resource_type = "Patient" GROUP BY source_id
+
+	//var sourceCred models.SourceCredential
+	//results := sr.gormClient.WithContext(ctx).
+	//	Where(models.SourceCredential{UserID: sr.GetCurrentUser(ctx).ID, ModelBase: models.ModelBase{ID: sourceUUID}}).
+	//	First(&sourceCred)
+
+	var wrappedResourceModels []models.ResourceFhir
+	results := sr.gormClient.WithContext(ctx).
+		Model(models.ResourceFhir{}).
+		Group("source_id").
+		Where(models.OriginBase{
+			UserID:             sr.GetCurrentUser(ctx).ID,
+			SourceResourceType: "Patient",
+		}).
+		Find(&wrappedResourceModels)
+
+	return wrappedResourceModels, results.Error
+}
+
+////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// SourceCredential
+////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+
+func (sr *sqliteRepository) CreateSource(ctx context.Context, sourceCreds *models.SourceCredential) error {
+	sourceCreds.UserID = sr.GetCurrentUser(ctx).ID
+
+	//Assign will **always** update the source credential in the DB with data passed into this function.
+	return sr.gormClient.WithContext(ctx).
+		Where(models.SourceCredential{
+			UserID:     sourceCreds.UserID,
+			SourceType: sourceCreds.SourceType,
+			Patient:    sourceCreds.Patient}).
+		Assign(*sourceCreds).FirstOrCreate(sourceCreds).Error
+}
+
+func (sr *sqliteRepository) GetSource(ctx context.Context, sourceId string) (*models.SourceCredential, error) {
+	sourceUUID, err := uuid.Parse(sourceId)
+	if err != nil {
+		return nil, err
+	}
+
+	var sourceCred models.SourceCredential
+	results := sr.gormClient.WithContext(ctx).
+		Where(models.SourceCredential{UserID: sr.GetCurrentUser(ctx).ID, ModelBase: models.ModelBase{ID: sourceUUID}}).
+		First(&sourceCred)
+
+	return &sourceCred, results.Error
+}
+
+func (sr *sqliteRepository) GetSourceSummary(ctx context.Context, sourceId string) (*models.SourceSummary, error) {
+	sourceUUID, err := uuid.Parse(sourceId)
+	if err != nil {
+		return nil, err
+	}
+
+	sourceSummary := &models.SourceSummary{}
+
+	source, err := sr.GetSource(ctx, sourceId)
+	if err != nil {
+		return nil, err
+	}
+	sourceSummary.Source = source
+
+	//group by resource type and return counts
+	// SELECT source_resource_type as resource_type, COUNT(*) as count FROM resource_fhirs WHERE source_id = "53c1e930-63af-46c9-b760-8e83cbc1abd9" GROUP BY source_resource_type;
+
+	var resourceTypeCounts []map[string]interface{}
+
+	result := sr.gormClient.WithContext(ctx).
+		Model(models.ResourceFhir{}).
+		Select("source_id, source_resource_type as resource_type, count(*) as count").
+		Group("source_resource_type").
+		Where(models.OriginBase{
+			UserID:   sr.GetCurrentUser(ctx).ID,
+			SourceID: sourceUUID,
+		}).
+		Scan(&resourceTypeCounts)
+
+	if result.Error != nil {
+		return nil, result.Error
+	}
+
+	sourceSummary.ResourceTypeCounts = resourceTypeCounts
+
+	//set patient
+	var wrappedPatientResourceModel models.ResourceFhir
+	results := sr.gormClient.WithContext(ctx).
+		Where(models.OriginBase{
+			UserID:             sr.GetCurrentUser(ctx).ID,
+			SourceResourceType: "Patient",
+			SourceID:           sourceUUID,
+		}).
+		First(&wrappedPatientResourceModel)
+
+	if results.Error != nil {
+		return nil, result.Error
+	}
+	sourceSummary.Patient = &wrappedPatientResourceModel
+
+	return sourceSummary, nil
+}
+
+func (sr *sqliteRepository) GetSources(ctx context.Context) ([]models.SourceCredential, error) {
+
+	var sourceCreds []models.SourceCredential
+	results := sr.gormClient.WithContext(ctx).
+		Where(models.SourceCredential{UserID: sr.GetCurrentUser(ctx).ID}).
+		Find(&sourceCreds)
+
+	return sourceCreds, results.Error
+}
+
+////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+// Utilities
+////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+
+func sqlitePragmaString(pragmas map[string]string) string {
+	q := url.Values{}
+	for key, val := range pragmas {
+		q.Add("_pragma", key+"="+val)
+	}
+
+	queryStr := q.Encode()
+	if len(queryStr) > 0 {
+		return "?" + queryStr
+	}
+	return ""
+}

backend/pkg/models/base.go

@@ -0,0 +1,50 @@
+package models
+
+import (
+	"github.com/google/uuid"
+	"gorm.io/gorm"
+	"time"
+)
+
+type ModelBase struct {
+	ID        uuid.UUID  `json:"id" gorm:"type:uuid;primary_key;"`
+	CreatedAt time.Time  `json:"created_at"`
+	UpdatedAt time.Time  `json:"updated_at"`
+	DeletedAt *time.Time `json:"deleted_at,omitempty" gorm:"index"`
+}
+
+//https://medium.com/@the.hasham.ali/how-to-use-uuid-key-type-with-gorm-cc00d4ec7100
+
+func (base *ModelBase) BeforeCreate(tx *gorm.DB) error {
+	base.ID = uuid.New()
+	return nil
+}
+
+type OriginBase struct {
+	ModelBase
+	User   *User     `json:"user,omitempty" gorm:"-"`
+	UserID uuid.UUID `json:"user_id"`
+
+	Source   *SourceCredential `json:"source,omitempty" gorm:"-"`
+	SourceID uuid.UUID         `json:"source_id" gorm:"not null;index:,unique,composite:source_resource_id"`
+
+	SourceResourceType string `json:"source_resource_type" gorm:"not null;index:,unique,composite:source_resource_id"`
+	SourceResourceID   string `json:"source_resource_id" gorm:"not null;index:,unique,composite:source_resource_id"`
+}
+
+func (o OriginBase) GetSourceID() uuid.UUID {
+	return o.SourceID
+}
+
+func (o OriginBase) GetSourceResourceType() string {
+	return o.SourceResourceType
+}
+func (o OriginBase) GetSourceResourceID() string {
+	return o.SourceResourceID
+}
+
+type OriginBaser interface {
+	GetSourceID() uuid.UUID
+	GetSourceResourceType() string
+	GetSourceResourceID() string
+}

backend/pkg/models/resource_fhir.go

@@ -0,0 +1,17 @@
+package models
+
+import (
+	"gorm.io/datatypes"
+)
+
+type ResourceFhir struct {
+	OriginBase
+
+	//embedded data
+	ResourceRaw datatypes.JSON `json:"resource_raw" gorm:"resource_raw"`
+}
+
+type ListResourceQueryOptions struct {
+	SourceID           string
+	SourceResourceType string
+}

backend/pkg/models/source_credential.go

@@ -0,0 +1,109 @@
+package models
+
+import (
+	"github.com/fastenhealth/fasten-sources/pkg"
+	"github.com/google/uuid"
+)
+
+// SourceCredential Data/Medical Provider Credentials
+// similar to LighthouseSourceDefinition from fasten-source
+type SourceCredential struct {
+	ModelBase
+	User       User           `json:"user,omitempty"`
+	UserID     uuid.UUID      `json:"user_id" gorm:"uniqueIndex:idx_user_source_patient"`
+	SourceType pkg.SourceType `json:"source_type" gorm:"uniqueIndex:idx_user_source_patient"`
+	Patient    string         `json:"patient" gorm:"uniqueIndex:idx_user_source_patient"`
+
+	//oauth endpoints
+	AuthorizationEndpoint string `json:"authorization_endpoint"`
+	TokenEndpoint         string `json:"token_endpoint"`
+	IntrospectionEndpoint string `json:"introspection_endpoint"`
+
+	Scopes                        []string `json:"scopes_supported" gorm:"type:text;serializer:json"`
+	Issuer                        string   `json:"issuer"`
+	GrantTypesSupported           []string `json:"grant_types_supported" gorm:"type:text;serializer:json"`
+	ResponseType                  []string `json:"response_types_supported" gorm:"type:text;serializer:json"`
+	ResponseModesSupported        []string `json:"response_modes_supported" gorm:"type:text;serializer:json"`
+	Audience                      string   `json:"aud"` //optional - required for some providers
+	CodeChallengeMethodsSupported []string `json:"code_challenge_methods_supported" gorm:"type:text;serializer:json"`
+
+	//Fasten custom configuration
+	UserInfoEndpoint   string `json:"userinfo_endpoint"`     //optional - supported by some providers, not others.
+	ApiEndpointBaseUrl string `json:"api_endpoint_base_url"` //api endpoint we'll communicate with after authentication
+	ClientId           string `json:"client_id"`
+	RedirectUri        string `json:"redirect_uri"` //lighthouse url the provider will redirect to (registered with App)
+
+	Confidential      bool `json:"confidential"`        //if enabled, requires client_secret to authenticate with provider (PKCE)
+	CORSRelayRequired bool `json:"cors_relay_required"` //if true, requires CORS proxy/relay, as provider does not return proper response to CORS preflight
+	//SecretKeyPrefix   string `json:"-"`                   //the secret key prefix to use, if empty (default) will use the sourceType value
+
+	// auth/credential data
+	AccessToken   string `json:"access_token"`
+	RefreshToken  string `json:"refresh_token"`
+	IdToken       string `json:"id_token"`
+	ExpiresAt     int64  `json:"expires_at"`
+	CodeChallenge string `json:"code_challenge"`
+	CodeVerifier  string `json:"code_verifier"`
+}
+
+func (s SourceCredential) GetSourceType() pkg.SourceType {
+	return s.SourceType
+}
+
+func (s SourceCredential) GetClientId() string {
+	return s.ClientId
+}
+
+func (s SourceCredential) GetPatientId() string {
+	return s.Patient
+}
+
+func (s SourceCredential) GetOauthAuthorizationEndpoint() string {
+	return s.AuthorizationEndpoint
+}
+
+func (s SourceCredential) GetOauthTokenEndpoint() string {
+	return s.TokenEndpoint
+}
+
+func (s SourceCredential) GetApiEndpointBaseUrl() string {
+	return s.ApiEndpointBaseUrl
+}
+
+func (s SourceCredential) GetRefreshToken() string {
+	return s.RefreshToken
+}
+
+func (s SourceCredential) GetAccessToken() string {
+	return s.AccessToken
+}
+
+func (s SourceCredential) GetExpiresAt() int64 {
+	return s.ExpiresAt
+}
+
+func (s SourceCredential) RefreshTokens(accessToken string, refreshToken string, expiresAt int64) {
+	if accessToken != s.AccessToken {
+		// update the "source" credential with new data (which will need to be sent
+		s.AccessToken = accessToken
+		s.ExpiresAt = expiresAt
+		// Don't overwrite `RefreshToken` with an empty value
+		// if this was a token refreshing request.
+		if refreshToken != "" {
+			s.RefreshToken = refreshToken
+		}
+	}
+}
+
+/*
+serverUrl: connectData.message.api_endpoint_base_url,
+clientId: connectData.message.client_id,
+redirectUri: connectData.message.redirect_uri,
+tokenUri: `${connectData.message.oauth_endpoint_base_url}/token`,
+scope: connectData.message.scopes.join(' '),
+tokenResponse: payload,
+expiresAt: getAccessTokenExpiration(payload, new BrowserAdapter()),
+codeChallenge: codeChallenge,
+codeVerifier: codeVerifier
+
+*/

backend/pkg/models/source_summary.go

@@ -0,0 +1,7 @@
+package models
+
+type SourceSummary struct {
+	Source             *SourceCredential        `json:"source,omitempty"`
+	ResourceTypeCounts []map[string]interface{} `json:"resource_type_counts,omitempty"`
+	Patient            *ResourceFhir            `json:"patient"`
+}

backend/pkg/models/summary.go

@@ -0,0 +1,7 @@
+package models
+
+type Summary struct {
+	Sources            []SourceCredential       `json:"sources"`
+	Patients           []ResourceFhir           `json:"patients"`
+	ResourceTypeCounts []map[string]interface{} `json:"resource_type_counts"`
+}

backend/pkg/models/user.go

@@ -1,7 +1,26 @@
 package models
 
+import "golang.org/x/crypto/bcrypt"
+
 type User struct {
+	ModelBase
 	FullName string `json:"full_name"`
-	Username string `json:"username"`
+	Username string `json:"username" gorm:"unique"`
 	Password string `json:"password"`
 }
+
+func (user *User) HashPassword(password string) error {
+	bytes, err := bcrypt.GenerateFromPassword([]byte(password), 14)
+	if err != nil {
+		return err
+	}
+	user.Password = string(bytes)
+	return nil
+}
+func (user *User) CheckPassword(providedPassword string) error {
+	err := bcrypt.CompareHashAndPassword([]byte(user.Password), []byte(providedPassword))
+	if err != nil {
+		return err
+	}
+	return nil
+}

backend/pkg/web/handler/auth.go

@@ -1,14 +1,13 @@
 package handler
 
 import (
+	"fmt"
+	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/auth"
 	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
 	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
 	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
 	"github.com/gin-gonic/gin"
-	jwt "github.com/golang-jwt/jwt/v4"
-	"log"
 	"net/http"
-	"time"
 )
 
 func AuthSignup(c *gin.Context) {
@@ -27,7 +26,7 @@ func AuthSignup(c *gin.Context) {
 	}
 
 	//TODO: we can derive the encryption key and the hash'ed user from the responseData sub. For now the Sub will be the user id prepended with hello.
-	userFastenToken, err := jwtGenerateFastenTokenFromUser(user, appConfig.GetString("jwt.issuer.key"))
+	userFastenToken, err := auth.JwtGenerateFastenTokenFromUser(user, appConfig.GetString("jwt.issuer.key"))
 
 	c.JSON(http.StatusOK, gin.H{"success": true, "data": userFastenToken})
 }
@@ -41,43 +40,21 @@ func AuthSignin(c *gin.Context) {
 		c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": err.Error()})
 		return
 	}
-	err := databaseRepo.VerifyUser(c, &user)
+
+	foundUser, err := databaseRepo.GetUserByEmail(c, user.Username)
+	if err != nil || foundUser == nil {
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": fmt.Sprintf("could not find user: %s", user.Username)})
+		return
+	}
+
+	err = foundUser.CheckPassword(user.Password)
 	if err != nil {
-		c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": err.Error()})
+		c.JSON(http.StatusUnauthorized, gin.H{"success": false, "error": fmt.Sprintf("username or password does not match: %s", user.Username)})
 		return
 	}
 
 	//TODO: we can derive the encryption key and the hash'ed user from the responseData sub. For now the Sub will be the user id prepended with hello.
-	userFastenToken, err := jwtGenerateFastenTokenFromUser(user, appConfig.GetString("jwt.issuer.key"))
+	userFastenToken, err := auth.JwtGenerateFastenTokenFromUser(user, appConfig.GetString("jwt.issuer.key"))
 
 	c.JSON(http.StatusOK, gin.H{"success": true, "data": userFastenToken})
 }
-
-type UserRegisteredClaims struct {
-	FullName string `json:"full_name"`
-	jwt.RegisteredClaims
-}
-
-func jwtGenerateFastenTokenFromUser(user models.User, issuerSigningKey string) (string, error) {
-	log.Printf("ISSUER KEY: " + issuerSigningKey)
-	userClaims := UserRegisteredClaims{
-		FullName: user.FullName,
-		RegisteredClaims: jwt.RegisteredClaims{
-			// In JWT, the expiry time is expressed as unix milliseconds
-			ExpiresAt: jwt.NewNumericDate(time.Now().Add(1 * time.Hour)),
-			IssuedAt:  jwt.NewNumericDate(time.Now()),
-			Issuer:    "docker-fastenhealth",
-			Subject:   user.Username,
-		},
-	}
-
-	//FASTEN_JWT_ISSUER_KEY
-	token := jwt.NewWithClaims(jwt.SigningMethodHS256, userClaims)
-	//token.Header["kid"] = "docker"
-	tokenString, err := token.SignedString([]byte(issuerSigningKey))
-
-	if err != nil {
-		return "", err
-	}
-	return tokenString, nil
-}

backend/pkg/web/handler/couchdb_proxy.go

@@ -1,40 +0,0 @@
-package handler
-
-import (
-	"fmt"
-	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
-	"github.com/gin-gonic/gin"
-	"log"
-	"net/http"
-	"net/http/httputil"
-	"net/url"
-	"strings"
-)
-
-func CouchDBProxy(c *gin.Context) {
-	appConfig := c.MustGet("CONFIG").(config.Interface)
-
-	couchdbUrl := fmt.Sprintf("%s://%s:%s", appConfig.GetString("couchdb.scheme"), appConfig.GetString("couchdb.host"), appConfig.GetString("couchdb.port"))
-	remote, err := url.Parse(couchdbUrl)
-	if err != nil {
-		panic(err)
-	}
-
-	proxy := httputil.NewSingleHostReverseProxy(remote)
-	//Define the director func
-	//This is a good place to log, for example
-	proxy.Director = func(req *http.Request) {
-		req.Header = c.Request.Header
-		req.Header.Add("X-Forwarded-Host", req.Host)
-		req.Header.Add("X-Origin-Host", remote.Host)
-		req.Host = remote.Host
-		req.URL.Scheme = remote.Scheme
-		req.URL.Host = remote.Host
-		log.Printf(c.Param("proxyPath"))
-		req.URL.Path = strings.TrimPrefix(c.Param("proxyPath"), "/database")
-
-		//todo: throw an error if not a user DB.
-	}
-
-	proxy.ServeHTTP(c.Writer, c.Request)
-}

backend/pkg/web/handler/resource_fhir.go

@@ -0,0 +1,51 @@
+package handler
+
+import (
+	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
+	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
+	"github.com/gin-gonic/gin"
+	"github.com/sirupsen/logrus"
+	"net/http"
+	"strings"
+)
+
+func ListResourceFhir(c *gin.Context) {
+	logger := c.MustGet("LOGGER").(*logrus.Entry)
+	databaseRepo := c.MustGet("REPOSITORY").(database.DatabaseRepository)
+
+	listResourceQueryOptions := models.ListResourceQueryOptions{}
+	if len(c.Query("sourceResourceType")) > 0 {
+		listResourceQueryOptions.SourceResourceType = c.Query("sourceResourceType")
+	}
+	if len(c.Query("sourceID")) > 0 {
+		listResourceQueryOptions.SourceID = c.Query("sourceID")
+	}
+
+	wrappedResourceModels, err := databaseRepo.ListResources(c, listResourceQueryOptions)
+
+	if err != nil {
+		logger.Errorln("An error occurred while retrieving resources", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false})
+		return
+	}
+
+	c.JSON(http.StatusOK, gin.H{"success": true, "data": wrappedResourceModels})
+}
+
+//this endpoint retrieves a specific resource by its ID
+func GetResourceFhir(c *gin.Context) {
+	logger := c.MustGet("LOGGER").(*logrus.Entry)
+	databaseRepo := c.MustGet("REPOSITORY").(database.DatabaseRepository)
+
+	resourceId := strings.Trim(c.Param("resourceId"), "/")
+	sourceId := strings.Trim(c.Param("sourceId"), "/")
+	wrappedResourceModel, err := databaseRepo.GetResourceBySourceId(c, sourceId, resourceId)
+
+	if err != nil {
+		logger.Errorln("An error occurred while retrieving resource", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false})
+		return
+	}
+
+	c.JSON(http.StatusOK, gin.H{"success": true, "data": wrappedResourceModel})
+}

backend/pkg/web/handler/source.go

@@ -0,0 +1,263 @@
+package handler
+
+import (
+	"fmt"
+	"github.com/fastenhealth/fasten-sources/clients/factory"
+	sourceModels "github.com/fastenhealth/fasten-sources/clients/models"
+	sourcePkg "github.com/fastenhealth/fasten-sources/pkg"
+	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
+	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
+	"github.com/gin-gonic/gin"
+	"github.com/sirupsen/logrus"
+	"io/ioutil"
+	"net/http"
+	"net/url"
+	"strings"
+)
+
+func CreateSource(c *gin.Context) {
+	logger := c.MustGet("LOGGER").(*logrus.Entry)
+	databaseRepo := c.MustGet("REPOSITORY").(database.DatabaseRepository)
+
+	sourceCred := models.SourceCredential{}
+	if err := c.ShouldBindJSON(&sourceCred); err != nil {
+		logger.Errorln("An error occurred while parsing posted source credential", err)
+		c.JSON(http.StatusBadRequest, gin.H{"success": false})
+		return
+	}
+
+	logger.Infof("Parsed Create SourceCredential Credentials Payload: %v", sourceCred)
+
+	err := databaseRepo.CreateSource(c, &sourceCred)
+	if err != nil {
+		logger.Errorln("An error occurred while storing source credential", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false})
+		return
+	}
+
+	// after creating the source, we should do a bulk import
+	summary, err := syncSourceResources(c, logger, databaseRepo, sourceCred)
+	if err != nil {
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false})
+		return
+	}
+
+	c.JSON(http.StatusOK, gin.H{"success": true, "source": sourceCred, "data": summary})
+}
+
+func SourceSync(c *gin.Context) {
+	logger := c.MustGet("LOGGER").(*logrus.Entry)
+	databaseRepo := c.MustGet("REPOSITORY").(database.DatabaseRepository)
+
+	logger.Infof("Get SourceCredential Credentials: %v", c.Param("sourceId"))
+
+	sourceCred, err := databaseRepo.GetSource(c, c.Param("sourceId"))
+	if err != nil {
+		logger.Errorln("An error occurred while retrieving source credential", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false})
+		return
+	}
+
+	// after creating the source, we should do a bulk import
+	summary, err := syncSourceResources(c, logger, databaseRepo, *sourceCred)
+	if err != nil {
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false})
+		return
+	}
+	c.JSON(http.StatusOK, gin.H{"success": true, "source": sourceCred, "data": summary})
+}
+
+func CreateManualSource(c *gin.Context) {
+	logger := c.MustGet("LOGGER").(*logrus.Entry)
+	databaseRepo := c.MustGet("REPOSITORY").(database.DatabaseRepository)
+
+	// single file
+	file, err := c.FormFile("file")
+	if err != nil {
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": "could not extract file from form"})
+		return
+	}
+	fmt.Printf("Uploaded filename: %s", file.Filename)
+
+	// create a temporary file to store this uploaded file
+	bundleFile, err := ioutil.TempFile("", file.Filename)
+	if err != nil {
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": "could not create temp file"})
+		return
+	}
+
+	// Upload the file to specific bundleFile.
+	err = c.SaveUploadedFile(file, bundleFile.Name())
+	if err != nil {
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": "could not save temp file"})
+		return
+	}
+
+	// We cannot save the "SourceCredential" object yet, as we do not know the patientID
+
+	// create a "manual" client, which we can use to parse the
+	manualSourceCredential := models.SourceCredential{
+		SourceType: sourcePkg.SourceTypeManual,
+	}
+	tempSourceClient, _, err := factory.GetSourceClient(sourcePkg.GetFastenEnv(), sourcePkg.SourceTypeManual, c, logger, manualSourceCredential)
+	if err != nil {
+		logger.Errorln("An error occurred while initializing hub client using manual source without credentials", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false})
+		return
+	}
+
+	patientId, bundleType, err := tempSourceClient.ExtractPatientId(bundleFile)
+	if err != nil {
+		logger.Errorln("An error occurred while extracting patient id", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": err.Error()})
+		return
+	}
+	manualSourceCredential.Patient = patientId
+
+	//store the manualSourceCredential
+	err = databaseRepo.CreateSource(c, &manualSourceCredential)
+	if err != nil {
+		logger.Errorln("An error occurred while creating manual source", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": err.Error()})
+		return
+	}
+
+	manualSourceClient, _, err := factory.GetSourceClient(sourcePkg.GetFastenEnv(), sourcePkg.SourceTypeManual, c, logger, manualSourceCredential)
+	if err != nil {
+		logger.Errorln("An error occurred while initializing hub client using manual source with credential", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false})
+		return
+	}
+
+	summary, err := manualSourceClient.SyncAllBundle(databaseRepo, bundleFile, bundleType)
+	if err != nil {
+		logger.Errorln("An error occurred while processing bundle", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": err.Error()})
+		return
+	}
+
+	c.JSON(http.StatusOK, gin.H{"success": true, "data": summary})
+}
+
+func GetSource(c *gin.Context) {
+	logger := c.MustGet("LOGGER").(*logrus.Entry)
+	databaseRepo := c.MustGet("REPOSITORY").(database.DatabaseRepository)
+
+	sourceCred, err := databaseRepo.GetSource(c, c.Param("sourceId"))
+	if err != nil {
+		logger.Errorln("An error occurred while retrieving source credential", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false})
+		return
+	}
+	c.JSON(http.StatusOK, gin.H{"success": true, "data": sourceCred})
+}
+
+func GetSourceSummary(c *gin.Context) {
+	logger := c.MustGet("LOGGER").(*logrus.Entry)
+	databaseRepo := c.MustGet("REPOSITORY").(database.DatabaseRepository)
+
+	sourceSummary, err := databaseRepo.GetSourceSummary(c, c.Param("sourceId"))
+	if err != nil {
+		logger.Errorln("An error occurred while retrieving source summary", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false})
+		return
+	}
+	c.JSON(http.StatusOK, gin.H{"success": true, "data": sourceSummary})
+}
+
+func ListSource(c *gin.Context) {
+	logger := c.MustGet("LOGGER").(*logrus.Entry)
+	databaseRepo := c.MustGet("REPOSITORY").(database.DatabaseRepository)
+
+	sourceCreds, err := databaseRepo.GetSources(c)
+	if err != nil {
+		logger.Errorln("An error occurred while listing source credentials", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false})
+		return
+	}
+	c.JSON(http.StatusOK, gin.H{"success": true, "data": sourceCreds})
+}
+
+func RawRequestSource(c *gin.Context) {
+	logger := c.MustGet("LOGGER").(*logrus.Entry)
+	databaseRepo := c.MustGet("REPOSITORY").(database.DatabaseRepository)
+
+	//!!!!!!INSECURE!!!!!!S
+	//We're setting the username to a user provided value, this is insecure, but required for calling databaseRepo fns
+	c.Set("AUTH_USERNAME", c.Param("username"))
+
+	foundSource, err := databaseRepo.GetSource(c, c.Param("sourceId"))
+	if err != nil {
+		logger.Errorf("An error occurred while finding source credential: %v", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": err.Error()})
+		return
+	}
+
+	if foundSource == nil {
+		logger.Errorf("Did not source credentials for %s", c.Param("sourceType"))
+		c.JSON(http.StatusNotFound, gin.H{"success": false, "error": err.Error()})
+		return
+	}
+
+	client, updatedSource, err := factory.GetSourceClient(sourcePkg.GetFastenEnv(), foundSource.SourceType, c, logger, foundSource)
+	if err != nil {
+		logger.Errorf("Could not initialize source client %v", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": err.Error()})
+		return
+	}
+	//TODO: if source has been updated, we should save the access/refresh token.
+	if updatedSource != nil {
+		logger.Warnf("TODO: source credential has been updated, we should store it in the database: %v", updatedSource)
+		//	err := databaseRepo.CreateSource(c, updatedSource)
+		//	if err != nil {
+		//		logger.Errorf("An error occurred while updating source credential %v", err)
+		//		c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": err.Error()})
+		//		return
+		//	}
+	}
+
+	var resp map[string]interface{}
+
+	parsedUrl, err := url.Parse(strings.TrimSuffix(c.Param("path"), "/"))
+	if err != nil {
+		logger.Errorf("Error parsing request, %v", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": err.Error()})
+		return
+	}
+	//make sure we include all query string parameters with the raw request.
+	parsedUrl.RawQuery = c.Request.URL.Query().Encode()
+
+	err = client.GetRequest(parsedUrl.String(), &resp)
+	if err != nil {
+		logger.Errorf("Error making raw request, %v", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": err.Error(), "data": resp})
+		return
+	}
+	c.JSON(http.StatusOK, gin.H{"success": true, "data": resp})
+}
+
+////// private functions
+func syncSourceResources(c *gin.Context, logger *logrus.Entry, databaseRepo database.DatabaseRepository, sourceCred models.SourceCredential) (sourceModels.UpsertSummary, error) {
+	// after creating the source, we should do a bulk import
+	sourceClient, updatedSource, err := factory.GetSourceClient(sourcePkg.GetFastenEnv(), sourceCred.SourceType, c, logger, sourceCred)
+	if err != nil {
+		logger.Errorln("An error occurred while initializing hub client using source credential", err)
+		return sourceModels.UpsertSummary{}, err
+	}
+	//TODO: update source
+	if updatedSource != nil {
+		logger.Warnf("TODO: source credential has been updated, we should store it in the database: %v", updatedSource)
+		//err := databaseRepo.CreateSource(c, updatedSource)
+		//if err != nil {
+		//	logger.Errorln("An error occurred while updating source credential", err)
+		//	return err
+		//}
+	}
+
+	summary, err := sourceClient.SyncAll(databaseRepo)
+	if err != nil {
+		logger.Errorln("An error occurred while bulk import of resources from source", err)
+		return summary, err
+	}
+	return summary, nil
+}

backend/pkg/web/handler/summary.go

@@ -0,0 +1,21 @@
+package handler
+
+import (
+	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
+	"github.com/gin-gonic/gin"
+	"github.com/sirupsen/logrus"
+	"net/http"
+)
+
+func GetSummary(c *gin.Context) {
+	logger := c.MustGet("LOGGER").(*logrus.Entry)
+	databaseRepo := c.MustGet("REPOSITORY").(database.DatabaseRepository)
+
+	summary, err := databaseRepo.GetSummary(c)
+	if err != nil {
+		logger.Errorln("An error occurred while retrieving summary", err)
+		c.JSON(http.StatusInternalServerError, gin.H{"success": false})
+		return
+	}
+	c.JSON(http.StatusOK, gin.H{"success": true, "data": summary})
+}

backend/pkg/web/middleware/require_auth.go

@@ -0,0 +1,47 @@
+package middleware
+
+import (
+	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/auth"
+	"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
+	"github.com/gin-gonic/gin"
+	"log"
+	"net/http"
+	"strings"
+)
+
+func RequireAuth() gin.HandlerFunc {
+	return func(c *gin.Context) {
+		appConfig := c.MustGet("CONFIG").(config.Interface)
+
+		authHeader := c.GetHeader("Authorization")
+		authHeaderParts := strings.Split(authHeader, " ")
+
+		if len(authHeaderParts) != 2 {
+			log.Println("Authentication header is invalid: " + authHeader)
+			c.JSON(http.StatusUnauthorized, gin.H{"success": false, "error": "request does not contain a valid token"})
+			c.Abort()
+			return
+		}
+
+		tokenString := authHeaderParts[1]
+
+		if tokenString == "" {
+			c.JSON(http.StatusUnauthorized, gin.H{"success": false, "error": "request does not contain an access token"})
+			c.Abort()
+			return
+		}
+		claim, err := auth.JwtValidateFastenToken(appConfig.GetString("jwt.issuer.key"), tokenString)
+		if err != nil {
+			c.JSON(http.StatusUnauthorized, gin.H{"success": false, "error": err.Error()})
+			c.Abort()
+			return
+		}
+
+		//todo, is this shared between all sessions??
+		c.Set("AUTH_TOKEN", tokenString)
+		c.Set("AUTH_USERNAME", claim.Subject)
+		c.Set("AUTH_USERID", claim.UserId)
+
+		c.Next()
+	}
+}

backend/pkg/web/server.go

@@ -42,10 +42,32 @@ func (ae *AppEngine) Setup(logger *logrus.Entry) *gin.Engine {
 
 			api.POST("/auth/signup", handler.AuthSignup)
 			api.POST("/auth/signin", handler.AuthSignin)
+			//
+			//r.Any("/database/*proxyPath", handler.CouchDBProxy)
+			//r.GET("/cors/*proxyPath", handler.CORSProxy)
+			//r.OPTIONS("/cors/*proxyPath", handler.CORSProxy)
 
-			r.Any("/database/*proxyPath", handler.CouchDBProxy)
-			r.GET("/cors/*proxyPath", handler.CORSProxy)
-			r.OPTIONS("/cors/*proxyPath", handler.CORSProxy)
+			secure := api.Group("/secure").Use(middleware.RequireAuth())
+			{
+				secure.GET("/summary", handler.GetSummary)
+
+				secure.POST("/source", handler.CreateSource)
+				secure.POST("/source/manual", handler.CreateManualSource)
+				secure.GET("/source", handler.ListSource)
+				secure.GET("/source/:sourceId", handler.GetSource)
+				secure.POST("/source/:sourceId/sync", handler.SourceSync)
+				secure.GET("/source/:sourceId/summary", handler.GetSourceSummary)
+				secure.GET("/resource/fhir", handler.ListResourceFhir) //
+				secure.GET("/resource/fhir/:sourceId/:resourceId", handler.GetResourceFhir)
+			}
+
+			if ae.Config.GetString("log.level") == "DEBUG" {
+				//in debug mode, this endpoint lets us request data directly from the source api
+				ae.Logger.Warningf("***INSECURE*** ***INSECURE*** DEBUG mode enables developer functionality, including unauthenticated raw api requests")
+
+				//http://localhost:9090/api/raw/test@test.com/436d7277-ad56-41ce-9823-44e353d1b3f6/Patient/smart-1288992
+				api.GET("/raw/:username/:sourceId/*path", handler.RawRequestSource)
+			}
 		}
 	}
 

config.yaml

@@ -22,4 +22,4 @@ web:
 
 log:
   file: '' #absolute or relative paths allowed, eg. web.log
-  level: INFO
+  level: DEBUG

frontend/angular.json

@@ -34,8 +34,7 @@
             ],
             "scripts": [
               "node_modules/@panva/oauth4webapi/build/index.js"
-            ],
-            "webWorkerTsConfig": "tsconfig.worker.json"
+            ]
           },
           "configurations": {
             "prod": {
@@ -161,8 +160,7 @@
             "styles": [
               "src/styles.scss"
             ],
-            "scripts": [],
-            "webWorkerTsConfig": "tsconfig.worker.json"
+            "scripts": []
           }
         },
         "lint": {

frontend/src/app/app-routing.module.ts

@@ -8,9 +8,9 @@ import {ResourceDetailComponent} from './pages/resource-detail/resource-detail.c
 import {AuthSigninComponent} from './pages/auth-signin/auth-signin.component';
 import {AuthSignupComponent} from './pages/auth-signup/auth-signup.component';
 import {IsAuthenticatedAuthGuard} from './auth-guards/is-authenticated-auth-guard';
-import {EncryptionEnabledAuthGuard} from './auth-guards/encryption-enabled.auth-guard';
 import {SourceDetailComponent} from './pages/source-detail/source-detail.component';
-import {EncryptionManagerComponent} from './pages/encryption-manager/encryption-manager.component';
+import {PatientProfileComponent} from './pages/patient-profile/patient-profile.component';
+import {MedicalHistoryComponent} from './pages/medical-history/medical-history.component';
 
 const routes: Routes = [
 
@@ -20,14 +20,15 @@ const routes: Routes = [
   { path: 'auth/signup/callback/:idp_type', component: AuthSignupComponent },
 
   { path: '', redirectTo: '/dashboard', pathMatch: 'full' },
-  { path: 'dashboard', component: DashboardComponent, canActivate: [ IsAuthenticatedAuthGuard, EncryptionEnabledAuthGuard] },
-  { path: 'source/:source_id', component: SourceDetailComponent, canActivate: [ IsAuthenticatedAuthGuard, EncryptionEnabledAuthGuard] },
-  { path: 'resource/:resource_id', component: ResourceDetailComponent, canActivate: [ IsAuthenticatedAuthGuard, EncryptionEnabledAuthGuard] },
-  { path: 'sources', component: MedicalSourcesComponent, canActivate: [ IsAuthenticatedAuthGuard, EncryptionEnabledAuthGuard] },
-  { path: 'sources/callback/:source_type', component: MedicalSourcesComponent, canActivate: [ IsAuthenticatedAuthGuard, EncryptionEnabledAuthGuard] },
+  { path: 'dashboard', component: DashboardComponent, canActivate: [ IsAuthenticatedAuthGuard] },
+  { path: 'source/:source_id', component: SourceDetailComponent, canActivate: [ IsAuthenticatedAuthGuard] },
+  { path: 'source/:source_id/resource/:resource_id', component: ResourceDetailComponent, canActivate: [ IsAuthenticatedAuthGuard] },
+  { path: 'sources', component: MedicalSourcesComponent, canActivate: [ IsAuthenticatedAuthGuard] },
+  { path: 'sources/callback/:source_type', component: MedicalSourcesComponent, canActivate: [ IsAuthenticatedAuthGuard] },
 
-  { path: 'account/security/manager', component: EncryptionManagerComponent, canActivate: [ IsAuthenticatedAuthGuard] },
 
+  { path: 'patient-profile', component: PatientProfileComponent, canActivate: [ IsAuthenticatedAuthGuard] },
+  { path: 'medical-history', component: MedicalHistoryComponent, canActivate: [ IsAuthenticatedAuthGuard] },
 
   // { path: 'general-pages', loadChildren: () => import('./general-pages/general-pages.module').then(m => m.GeneralPagesModule) },
   // { path: 'ui-elements', loadChildren: () => import('./ui-elements/ui-elements.module').then(m => m.UiElementsModule) },

frontend/src/app/app.component.ts

@@ -2,7 +2,6 @@ import { Component, OnInit } from '@angular/core';
 import {NavigationEnd, Router} from '@angular/router';
 import {fromWorker} from 'observable-webworker';
 import {Observable, of} from 'rxjs';
-import {QueueService} from './workers/queue.service';
 import {ToastService} from './services/toast.service';
 
 @Component({
@@ -17,7 +16,7 @@ export class AppComponent implements OnInit {
   showHeader:boolean = false;
   showFooter:boolean = true;
 
-  constructor(private router: Router, private queueService: QueueService, private toastService: ToastService) {}
+  constructor(private router: Router, private toastService: ToastService) {}
 
   ngOnInit() {
 

frontend/src/app/app.module.ts

@@ -19,15 +19,15 @@ import { AuthSigninComponent } from './pages/auth-signin/auth-signin.component';
 import { FormsModule } from '@angular/forms';
 import { NgxDropzoneModule } from 'ngx-dropzone';
 import { IsAuthenticatedAuthGuard } from './auth-guards/is-authenticated-auth-guard';
-import { EncryptionEnabledAuthGuard } from './auth-guards/encryption-enabled.auth-guard';
-import {FastenDbService} from './services/fasten-db.service';
+import {FastenApiService} from './services/fasten-api.service';
 import {Router} from '@angular/router';
 import { SourceDetailComponent } from './pages/source-detail/source-detail.component';
 import { HighlightModule, HIGHLIGHT_OPTIONS } from 'ngx-highlightjs';
 import {AuthInterceptorService} from './services/auth-interceptor.service';
 import { MomentModule } from 'ngx-moment';
-import { EncryptionManagerComponent } from './pages/encryption-manager/encryption-manager.component';
 import {AuthService} from './services/auth.service';
+import { PatientProfileComponent } from './pages/patient-profile/patient-profile.component';
+import { MedicalHistoryComponent } from './pages/medical-history/medical-history.component';
 
 @NgModule({
   declarations: [
@@ -40,7 +40,8 @@ import {AuthService} from './services/auth.service';
     AuthSignupComponent,
     AuthSigninComponent,
     SourceDetailComponent,
-    EncryptionManagerComponent,
+    PatientProfileComponent,
+    MedicalHistoryComponent,
   ],
   imports: [
     FormsModule,
@@ -63,7 +64,6 @@ import {AuthService} from './services/auth.service';
       deps: [AuthService, Router]
     },
     IsAuthenticatedAuthGuard,
-    EncryptionEnabledAuthGuard,
     {
       provide: HIGHLIGHT_OPTIONS,
       useValue: {

frontend/src/app/auth-guards/encryption-enabled.auth-guard.ts

@@ -1,19 +0,0 @@
-import { Injectable } from '@angular/core';
-import {CanActivate, ActivatedRouteSnapshot, RouterStateSnapshot, UrlTree, Router} from '@angular/router';
-import {FastenDbService} from '../services/fasten-db.service';
-
-@Injectable()
-export class EncryptionEnabledAuthGuard implements CanActivate {
-  constructor(private fastenDbService: FastenDbService, private router: Router) {
-
-  }
-
-  async canActivate(route: ActivatedRouteSnapshot, state: RouterStateSnapshot): Promise <boolean> {
-    //check if the user has encryption data stored in this browser already
-    if (!await this.fastenDbService.isCryptConfigAvailable()) {
-      return await this.router.navigate(['/account/security/manager']);
-    }
-    // continue as normal
-    return true
-  }
-}

frontend/src/app/components/header/header.component.ts

@@ -1,5 +1,4 @@
 import { Component, OnInit } from '@angular/core';
-import {FastenDbService} from '../../services/fasten-db.service';
 import { Router } from '@angular/router';
 import {AuthService} from '../../services/auth.service';
 import {UserRegisteredClaims} from '../../models/fasten/user-registered-claims';

frontend/src/app/components/list-fallback-resource/list-fallback-resource.component.html

@@ -9,6 +9,6 @@
 
 <ul class="list-group">
   <li class="list-group-item" *ngFor="let resource of resourceList">
-    <a routerLink="/resource/{{resource.base64Id()}}">{{resource.source_resource_id}}</a>
+    <a routerLink="/source/{{resource.source_id}}/resource/{{resource.source_resource_id}}">{{resource.source_resource_id}}</a>
   </li>
 </ul>

frontend/src/app/components/list-fallback-resource/list-fallback-resource.component.ts

@@ -1,8 +1,7 @@
 import {ChangeDetectorRef, Component, Input, OnInit} from '@angular/core';
-import {ResourceFhir} from '../../../lib/models/database/resource_fhir';
+import {ResourceFhir} from '../../models/fasten/resource_fhir';
 import {ResourceListComponentInterface} from '../list-generic-resource/list-generic-resource.component';
 import {Router} from '@angular/router';
-import {Base64} from '../../../lib/utils/base64';
 
 @Component({
   selector: 'app-list-fallback-resource',

frontend/src/app/components/list-generic-resource/list-generic-resource.component.ts

@@ -1,9 +1,8 @@
 import {ChangeDetectorRef, Component, Input, OnInit, ViewChild} from '@angular/core';
 import {DatatableComponent, ColumnMode, SelectionType} from '@swimlane/ngx-datatable';
-import {ResourceFhir} from '../../../lib/models/database/resource_fhir';
+import {ResourceFhir} from '../../models/fasten/resource_fhir';
 import {FORMATTERS, getPath, obsValue, attributeXTime} from './utils';
 import {Router} from '@angular/router';
-import {Base64} from '../../../lib/utils/base64';
 
 //all Resource list components must implement this Interface
 export interface ResourceListComponentInterface {
@@ -61,7 +60,6 @@ export class ListGenericResourceComponent implements OnInit, ResourceListCompone
 
     this.rows = this.resourceList.map((resource) => {
       let row = {
-        _id: resource._id,
         source_id: resource.source_id,
         source_resource_type: resource.source_resource_type,
         source_resource_id: resource.source_resource_id
@@ -87,7 +85,8 @@ export class ListGenericResourceComponent implements OnInit, ResourceListCompone
    */
   onSelect({ selected }) {
     console.log('Select Event', selected);
-    this.router.navigateByUrl(`/resource/${Base64.Encode(selected[0]._id)}`);
+    this.router.navigateByUrl(`/source/${selected[0].source_id}/resource/${selected[0].source_resource_id}`);
+
   }
 
 }

frontend/src/app/components/resource-list/resource-list.component.ts

@@ -1,8 +1,8 @@
 import {ChangeDetectionStrategy, Component, Input, OnChanges, OnInit, SimpleChanges, Type, ViewChild} from '@angular/core';
-import {FastenDbService} from '../../services/fasten-db.service';
-import {Source} from '../../../lib/models/database/source';
+import {FastenApiService} from '../../services/fasten-api.service';
+import {Source} from '../../models/fasten/source';
 import {Observable, of} from 'rxjs';
-import {ResourceFhir} from '../../../lib/models/database/resource_fhir';
+import {ResourceFhir} from '../../models/fasten/resource_fhir';
 import {ListAdverseEventComponent} from '../list-generic-resource/list-adverse-event.component';
 import {ListCommunicationComponent} from '../list-generic-resource/list-communication.component';
 import {ListConditionComponent} from '../list-generic-resource/list-condition.component';
@@ -49,7 +49,7 @@ export class ResourceListComponent implements OnInit, OnChanges {
   @ViewChild(ResourceListOutletDirective, {static: true}) resourceListOutlet!: ResourceListOutletDirective;
 
 
-  constructor(private fastenDb: FastenDbService) { }
+  constructor(private fastenApi: FastenApiService) { }
 
   ngOnInit(): void {
     this.loadComponent()
@@ -63,7 +63,7 @@ export class ResourceListComponent implements OnInit, OnChanges {
     const viewContainerRef = this.resourceListOutlet.viewContainerRef;
     viewContainerRef.clear();
 
-    this.getResources().then((resourceList) => {
+    this.getResources().subscribe((resourceList) => {
       let componentType = this.typeLookup(this.resourceListType)
       if(componentType != null){
         console.log("Attempting to create component", this.resourceListType, componentType)
@@ -75,19 +75,18 @@ export class ResourceListComponent implements OnInit, OnChanges {
     })
   }
 
-  getResources(): Promise<ResourceFhir[]>{
+  getResources(): Observable<ResourceFhir[]>{
 
     if(this.resourceListType && !this.resourceListCache[this.resourceListType]){
       // this resource type list has not been downloaded yet, do so now
-      return this.fastenDb.GetResourcesForSource(this.source._id, this.resourceListType)
-        .then((paginatedResponse) => {
-          let resourceList = paginatedResponse.rows as ResourceFhir[]
+      return this.fastenApi.getResources(this.resourceListType, this.source.id)
+        .pipe(map((resourceList: ResourceFhir[]) => {
           //cache this response so we can skip the request next time
           this.resourceListCache[this.resourceListType] = resourceList
           return resourceList
-        })
+        }))
     } else {
-      return Promise.resolve(this.resourceListCache[this.resourceListType] || [])
+      return of(this.resourceListCache[this.resourceListType] || [])
     }
   }
 

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

@@ -0,0 +1,48 @@
+export class ResourceFhir {
+  user_id?: string
+  source_id: string = ""
+  source_resource_type: string = ""
+  source_resource_id: string = ""
+
+  fhir_version: string = ""
+  resource_raw: IResourceRaw
+
+  constructor(object?: any) {
+    return Object.assign(this, object)
+  }
+}
+
+
+//This is the "raw" Fhir resource
+export interface IResourceRaw {
+  resourceType: string
+  id?: string
+  meta?: IResourceMetaRaw
+}
+// This is the "raw" Fhir Bundle resource
+export interface IResourceBundleRaw {
+  resourceType: string
+  id?: string
+  entry: IResourceBundleEntryRaw[]
+  total?: number
+  link?: IResourceBundleLinkRaw[]
+  meta?: IResourceMetaRaw
+}
+
+export interface IResourceBundleLinkRaw {
+  id?: string
+  relation: string
+  url: string
+}
+
+export interface IResourceBundleEntryRaw {
+  id?: string
+  fullUrl?: string
+  resource: IResourceRaw
+}
+
+export interface IResourceMetaRaw {
+  id?: string
+  versionId?: string
+  lastUpdated: string
+}

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

@@ -1,5 +1,5 @@
-import {Source} from '../database/source';
-import {ResourceFhir} from '../database/resource_fhir';
+import {Source} from './source';
+import {ResourceFhir} from './resource_fhir';
 
 export class ResourceTypeCounts {
   count: number

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

@@ -0,0 +1,18 @@
+import {LighthouseSourceMetadata} from '../lighthouse/lighthouse-source-metadata';
+
+export class Source extends LighthouseSourceMetadata{
+  id?: string
+  user_id?: number
+  source_type: string
+
+  patient: string
+  access_token:          string
+  refresh_token?:         string
+  id_token?:              string
+  expires_at:            number //seconds since epoch
+
+  constructor(object: any) {
+    super()
+    return Object.assign(this, object)
+  }
+}

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

@@ -1,6 +1,6 @@
-import {Source} from '../database/source';
+import {Source} from './source';
 import {ResourceTypeCounts} from './source-summary';
-import {ResourceFhir} from '../database/resource_fhir';
+import {ResourceFhir} from './resource_fhir';
 
 export class Summary {
   sources: Source[]

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

@@ -1,4 +1,5 @@
 export class User {
+  user_id?: number
   full_name?: string
   username?: string
   password?: string

frontend/src/app/models/queue/source-sync-message.ts

@@ -1,4 +1,4 @@
-import {Source} from '../../../lib/models/database/source';
+import {Source} from '../../models/fasten/source';
 
 export class SourceSyncMessage {
   source: Source

frontend/src/app/pages/auth-signin/auth-signin.component.ts

@@ -1,13 +1,11 @@
 import {Component, OnInit} from '@angular/core';
-import {User} from '../../../lib/models/fasten/user';
-import {FastenDbService} from '../../services/fasten-db.service';
+import {User} from '../../models/fasten/user';
 import {ActivatedRoute, Router} from '@angular/router';
 import {ToastService} from '../../services/toast.service';
 import {ToastNotification, ToastType} from '../../models/fasten/toast';
 import {environment} from '../../../environments/environment';
 import {AuthService} from '../../services/auth.service';
 import {Location} from '@angular/common';
-import {PouchdbCrypto} from '../../../lib/database/plugins/crypto';
 
 @Component({
   selector: 'app-auth-signin',
@@ -23,7 +21,6 @@ export class AuthSigninComponent implements OnInit {
   loading: boolean = false
 
   constructor(
-    private fastenDb: FastenDbService,
     private authService: AuthService,
     private router: Router,
     private route: ActivatedRoute,
@@ -47,10 +44,7 @@ export class AuthSigninComponent implements OnInit {
           //TODO: replace Pouchdb.
           let userId = this.authService.GetCurrentUser().sub
           //TODO: static IV, must be removed/replaced.
-          return {username: userId, key: userId, config: "WyI3NUhJcEhZTXBNVXRtMHlJcnBMckhRPT0iLHsic2FsdExlbmd0aCI6MTYsIm1lbW9yeVNpemUiOjQwOTYsIml0ZXJhdGlvbnMiOjEwMCwicGFyYWxsZWxpc20iOjF9XQ=="}
-        })
-        .then((cryptoConfig) => {
-          PouchdbCrypto.StoreCryptConfig(cryptoConfig)
+          return {username: userId, key: userId}
         })
         .then(() => this.router.navigateByUrl('/dashboard'))
         .catch((err)=>{

frontend/src/app/pages/auth-signup/auth-signup.component.ts

@@ -1,6 +1,5 @@
 import { Component, OnInit } from '@angular/core';
-import {FastenDbService} from '../../services/fasten-db.service';
-import {User} from '../../../lib/models/fasten/user';
+import {User} from '../../models/fasten/user';
 import {Router} from '@angular/router';
 import {ToastNotification, ToastType} from '../../models/fasten/toast';
 import {ToastService} from '../../services/toast.service';

frontend/src/app/pages/dashboard/dashboard.component.html

@@ -148,7 +148,7 @@
                     <div class="media-body">
                       <h5>{{metadataSource[source.source_type]?.display}}</h5>
                       <p>
-                        {{getPatientSummary(patientForSource[source._id]?.resource_raw)}}
+                        {{getPatientSummary(patientForSource[source.id]?.resource_raw)}}
                       </p>
 
                     </div>

frontend/src/app/pages/dashboard/dashboard.component.ts

@@ -1,12 +1,11 @@
 import { Component, OnInit } from '@angular/core';
-import {Source} from '../../../lib/models/database/source';
+import {Source} from '../../models/fasten/source';
 import {Router} from '@angular/router';
-import {ResourceFhir} from '../../../lib/models/database/resource_fhir';
+import {ResourceFhir} from '../../models/fasten/resource_fhir';
 import {forkJoin} from 'rxjs';
 import {MetadataSource} from '../../models/fasten/metadata-source';
-import {FastenDbService} from '../../services/fasten-db.service';
-import {Summary} from '../../../lib/models/fasten/summary';
-import {Base64} from '../../../lib/utils/base64';
+import {FastenApiService} from '../../services/fasten-api.service';
+import {Summary} from '../../models/fasten/summary';
 import {LighthouseService} from '../../services/lighthouse.service';
 
 @Component({
@@ -25,7 +24,7 @@ export class DashboardComponent implements OnInit {
 
   constructor(
     private lighthouseApi: LighthouseService,
-    private fastenDb: FastenDbService,
+    private fastenApi: FastenApiService,
     private router: Router
   ) { }
 
@@ -49,7 +48,7 @@ export class DashboardComponent implements OnInit {
     //     })
     //   })
 
-    forkJoin([this.fastenDb.GetSummary(), this.lighthouseApi.getLighthouseSourceMetadataMap()]).subscribe(results => {
+    forkJoin([this.fastenApi.getSummary(), this.lighthouseApi.getLighthouseSourceMetadataMap()]).subscribe(results => {
       let summary = results[0] as Summary
       let metadataSource = results[1] as { [name: string]: MetadataSource }
 
@@ -81,7 +80,7 @@ export class DashboardComponent implements OnInit {
   }
 
   selectSource(selectedSource: Source){
-    this.router.navigateByUrl(`/source/${Base64.Encode(selectedSource._id)}`, {
+    this.router.navigateByUrl(`/source/${selectedSource.id}`, {
       state: selectedSource
     });
   }

frontend/src/app/pages/encryption-manager/encryption-manager.component.html

@@ -1,151 +0,0 @@
-<div class="az-content az-content-profile">
-  <div class="container">
-    <div class="row w-100">
-      <div class="col-sm-12">
-        <h2 class="az-content-title mg-t-20">Security Manager</h2>
-        <p class="mb-5">
-          Before you use Fasten you'll need to import or generate a new encryption key.
-          <br/>
-          <br/>
-          Fasten uses <a href="https://en.wikipedia.org/wiki/Zero-knowledge_service" target="_blank">zero-knowledge encryption</a> to secure your medical data.
-          This means that your medical records are encrypted on your device, before they are stored in the Fasten database.
-          The encrypted data stored in the database is worthless without your encryption key.
-          <br/>
-          <br/>
-          You must safely store your encryption key as you would a username & password,
-          as it's the only thing that will allow you to access your records.</p>
-
-        <div *ngIf="cryptoPanel == CryptoPanelType.Generate" class="wizard clearfix">
-          <div class="steps clearfix">
-            <ul role="tablist">
-              <li role="tab" class="first" [ngClass]="{'current': currentStep == 1, 'disabled': currentStep != 1}">
-                <a aria-controls="wizard1-p-0">
-                  <span class="number">1</span>
-                  <span class="title">Download</span></a>
-              </li>
-              <li role="tab" class="last" [ngClass]="{'current': currentStep == 2, 'disabled': currentStep != 2}">
-                <a aria-controls="wizard1-p-2">
-                  <span class="number">2</span>
-                  <span class="title">Validate</span>
-                </a>
-              </li>
-            </ul>
-          </div>
-          <div class="content clearfix">
-            <ng-container [ngSwitch]="currentStep">
-              <ng-container *ngSwitchCase="1">
-                <h3 tabindex="-1" class="title current">Generate an encryption key</h3>
-                <section role="tabpanel" aria-labelledby="wizard1-h-0" class="body current" aria-hidden="false">
-                  <p class="mg-b-0">
-                    Fasten has generated an encryption key for you. You can use this encryption key to decode your medical records on this browser, and other devices.
-                    <br/>
-
-                    This is the only time the encryption key will be available to view, copy or download. We recommend downloading this key and storing the file in a secure location.
-                    <br/>
-                    You can reset your encryption key at any time, however any previously encrypted data will no longer be accessible.
-                  </p>
-
-                  <pre><code [highlight]="currentCryptoConfig | json"></code></pre>
-
-                  <div class="row row-xs wd-xl-80p">
-                    <div class="col-sm-6 col-md-3">
-                      <a [href]="generateCryptoConfigUrl" [download]="generateCryptoConfigFilename" class="btn btn-warning btn-rounded btn-block">Download Encryption Key</a>
-                    </div>
-                  </div>
-                </section>
-              </ng-container>
-              <ng-container *ngSwitchCase="2">
-                <h3 tabindex="-1" class="title current">Validate your encryption key</h3>
-                <section role="tabpanel" aria-labelledby="wizard1-h-0" class="body current" aria-hidden="false">
-                  <p class="mg-b-10">
-                    Please select your encryption key (which you generated in the previous step) using the file input below.
-                    <br/>
-                    It'll be validated against your browser's encryption key to ensure fidelity.
-                  </p>
-
-                  <div class="row">
-                    <div class="col-4">
-                      <div class="custom-file">
-                        <input type="file" class="custom-file-input" id="generateCustomFile" (change)="generateOpenFileHandler($event.target.files)" accept="application/json">
-                        <label class="custom-file-label" for="generateCustomFile">Choose file</label>
-                        <div *ngIf="generateCustomFileError" class="alert alert-danger">
-                          {{generateCustomFileError}}
-                        </div>
-                      </div>
-                    </div>
-                  </div>
-                </section>
-              </ng-container>
-
-            </ng-container>
-          </div>
-          <div *ngIf="currentStep != lastStep" class="actions clearfix">
-            <ul role="menu" aria-label="Pagination">
-              <li class="disabled" aria-disabled="true"></li>
-              <li aria-disabled="false"><button class="btn btn-az-primary btn-block" (click)="nextHandler()" role="menuitem">Next</button></li>
-            </ul>
-          </div>
-        </div>
-
-
-        <div *ngIf="cryptoPanel == CryptoPanelType.Import" class="wizard clearfix">
-          <div class="steps clearfix">
-            <ul role="tablist">
-              <li role="tab" class="first" [ngClass]="{'current': currentStep == 1, 'disabled': currentStep != 1}">
-                <a aria-controls="wizard1-p-0">
-                  <span class="number">1</span>
-                  <span class="title">Import</span></a>
-              </li>
-              <li role="tab" class="last" [ngClass]="{'current': currentStep == 2, 'disabled': currentStep != 2}">
-                <a aria-controls="wizard1-p-2">
-                  <span class="number">2</span>
-                  <span class="title">Validate</span>
-                </a>
-              </li>
-            </ul>
-          </div>
-          <div class="content clearfix">
-            <ng-container [ngSwitch]="currentStep">
-              <ng-container *ngSwitchCase="1">
-                <h3 tabindex="-1" class="title current">Import existing encryption key</h3>
-                <section role="tabpanel" aria-labelledby="wizard1-h-0" class="body current" aria-hidden="false">
-                  <p class="mg-b-10">
-                    Fasten was unable to find your encryption key on this device, and has detected encrypted data in your database.
-                    <br/>
-                    You will need to provide your encryption key to access your health records.
-                  </p>
-
-                  <div class="row">
-                    <div class="col-4">
-                      <div class="custom-file">
-                        <input type="file" class="custom-file-input" id="importCustomFile" (change)="importOpenFileHandler($event.target.files)" accept="application/json">
-                        <label class="custom-file-label" for="importCustomFile">Choose file</label>
-                        <div *ngIf="importCustomFileError" class="alert alert-danger">
-                          {{importCustomFileError}}
-                        </div>
-                      </div>
-                    </div>
-                  </div>
-
-                </section>
-              </ng-container>
-              <ng-container *ngSwitchCase="2">
-                <h3 tabindex="-1" class="title current">Validate encryption key</h3>
-                <section role="tabpanel" aria-labelledby="wizard1-h-0" class="body current" aria-hidden="false">
-                  <p class="mg-b-10">
-                    Thank you for providing your encryption key. Fasten will attempt to decrypt your secured records with this key.
-                  </p>
-                  <div class="spinner-border" role="status">
-                    <span class="sr-only">Loading...</span>
-                  </div>
-                </section>
-              </ng-container>
-            </ng-container>
-          </div>
-
-        </div>
-      </div>
-    </div>
-
-  </div>
-</div>

frontend/src/app/pages/encryption-manager/encryption-manager.component.spec.ts

@@ -1,26 +0,0 @@
-import { ComponentFixture, TestBed } from '@angular/core/testing';
-
-import { EncryptionManagerComponent } from './encryption-manager.component';
-import {HttpClientTestingModule} from '@angular/common/http/testing';
-
-describe('EncryptionManagerComponent', () => {
-  let component: EncryptionManagerComponent;
-  let fixture: ComponentFixture<EncryptionManagerComponent>;
-
-  beforeEach(async () => {
-    await TestBed.configureTestingModule({
-      declarations: [ EncryptionManagerComponent ],
-      imports: [HttpClientTestingModule],
-
-    })
-    .compileComponents();
-
-    fixture = TestBed.createComponent(EncryptionManagerComponent);
-    component = fixture.componentInstance;
-    fixture.detectChanges();
-  });
-
-  it('should create', () => {
-    expect(component).toBeTruthy();
-  });
-});

frontend/src/app/pages/encryption-manager/encryption-manager.component.ts

@@ -1,198 +0,0 @@
-import { Component, OnInit } from '@angular/core';
-import { v4 as uuidv4 } from 'uuid';
-import {PouchdbCryptConfig, PouchdbCrypto} from '../../../lib/database/plugins/crypto';
-import {FastenDbService} from '../../services/fasten-db.service';
-import {DomSanitizer, SafeResourceUrl} from '@angular/platform-browser';
-import {Router} from '@angular/router';
-import {ToastService} from '../../services/toast.service';
-import {ToastNotification, ToastType} from '../../models/fasten/toast';
-
-export enum CryptoPanelType {
-  Loading,
-  Import,
-  Generate,
-}
-
-
-@Component({
-  selector: 'app-encryption-manager',
-  templateUrl: './encryption-manager.component.html',
-  styleUrls: ['./encryption-manager.component.scss']
-})
-export class EncryptionManagerComponent implements OnInit {
-  CryptoPanelType = CryptoPanelType
-  cryptoPanel: CryptoPanelType = CryptoPanelType.Loading
-  currentCryptoConfig: PouchdbCryptConfig = null
-
-  generateCryptoConfigUrl: SafeResourceUrl = ""
-  generateCryptoConfigFilename: string = ""
-  generateCustomFileError: string = ""
-
-  importCustomFileError: string = ""
-
-  currentStep: number
-  lastStep: number
-
-
-  constructor(private fastenDbService: FastenDbService, private sanitizer: DomSanitizer, private router: Router, private toastService: ToastService) { }
-
-  ngOnInit(): void {
-
-    this.fastenDbService.IsDatabasePopulated()
-      .then((isPopulated) => {
-        if(isPopulated){
-          return this.showImportCryptoConfig()
-        } else {
-          return this.showGenerateCryptoConfig()
-        }
-      })
-
-  }
-
-  nextHandler() {
-    this.currentStep += 1
-    // if (!this.stepsService.isLastStep()) {
-    //   this.stepsService.moveToNextStep();
-    // } else {
-    //   this.onSubmit();
-    // }
-  }
-
-  /////////////////////////////////////////////////////////////////////////////////////////////////
-  // Generate Wizard Methods
-  /////////////////////////////////////////////////////////////////////////////////////////////////
-  async showGenerateCryptoConfig(): Promise<PouchdbCryptConfig> {
-    this.cryptoPanel = CryptoPanelType.Generate
-    this.currentStep = 1
-    this.lastStep = 2
-    if(!this.currentCryptoConfig){
-      this.currentCryptoConfig = await PouchdbCrypto.CryptConfig(uuidv4(), this.fastenDbService.current_user)
-      await PouchdbCrypto.StoreCryptConfig(this.currentCryptoConfig) //store in indexdb
-
-
-      //generate URL for downloading.
-      let currentCryptoConfigBlob = new Blob([JSON.stringify(this.currentCryptoConfig)], { type: 'application/json' });
-      this.generateCryptoConfigUrl = this.sanitizer.bypassSecurityTrustResourceUrl(window.URL.createObjectURL(currentCryptoConfigBlob));
-      this.generateCryptoConfigFilename = `fasten-${this.fastenDbService.current_user}.key.json`
-    }
-
-    return this.currentCryptoConfig
-  }
-
-  generateOpenFileHandler(fileList: FileList) {
-    this.generateCustomFileError = ""
-    let file = fileList[0];
-    this.readFileContent(file)
-      .then((content) => {
-        let parsedCryptoConfig = JSON.parse(content) as PouchdbCryptConfig
-
-        //check if the parsed encryption key matches the currently set encryption key
-
-        if(parsedCryptoConfig.key == this.currentCryptoConfig.key &&
-          parsedCryptoConfig.username == this.currentCryptoConfig.username &&
-          parsedCryptoConfig.config == this.currentCryptoConfig.config){
-          return true
-        } else {
-          //throw an error & notify user
-          this.generateCustomFileError = "Crypto configuration file does not match"
-          throw new Error(this.generateCustomFileError)
-        }
-      })
-      .then(() => {
-
-        const toastNotification = new ToastNotification()
-        toastNotification.type = ToastType.Success
-        toastNotification.message = "Successfully validated & stored encryption key."
-        toastNotification.autohide = true
-        this.toastService.show(toastNotification)
-
-        //redirect user to dashboard
-        return this.router.navigate(['/dashboard']);
-      })
-      .catch((err) => {
-        // delete invalid encryption key
-        this.currentStep = 1
-        return PouchdbCrypto.DeleteCryptConfig(this.fastenDbService.current_user)
-          .then(() => {
-            //an error occurred while importing credential
-            const toastNotification = new ToastNotification()
-            toastNotification.type = ToastType.Error
-            toastNotification.message = "Provided encryption key does not match. Generating new encryption key, please store it and try again."
-            toastNotification.autohide = false
-            this.toastService.show(toastNotification)
-          })
-      })
-  }
-
-  /////////////////////////////////////////////////////////////////////////////////////////////////
-  // Import Wizard Methods
-  /////////////////////////////////////////////////////////////////////////////////////////////////
-
-  async showImportCryptoConfig(): Promise<any> {
-    this.cryptoPanel = CryptoPanelType.Import
-    this.currentStep = 1
-    this.lastStep = 2
-  }
-
-  importOpenFileHandler(fileList: FileList) {
-    this.importCustomFileError = ""
-    let file = fileList[0];
-    this.readFileContent(file)
-      .then((content) => {
-        let cryptoConfig = JSON.parse(content) as PouchdbCryptConfig
-
-        if(!cryptoConfig.key || !cryptoConfig.config){
-          this.importCustomFileError = "Invalid crypto configuration file"
-          throw new Error(this.importCustomFileError)
-        }
-
-        return PouchdbCrypto.StoreCryptConfig(cryptoConfig)
-      })
-      .then(() => {
-        //go to step 2
-        this.currentStep = 2
-        //attempt to initialize pouchdb with specified crypto
-        this.fastenDbService.ResetDB()
-        return this.fastenDbService.GetSources()
-
-      })
-      .then(() => {
-        const toastNotification = new ToastNotification()
-        toastNotification.type = ToastType.Success
-        toastNotification.message = "Successfully validated & imported encryption key."
-        toastNotification.autohide = true
-        this.toastService.show(toastNotification)
-
-        return this.router.navigate(['/dashboard']);
-      })
-      .catch((err) => {
-        console.error(err)
-        // delete invalid encryption key
-        this.currentStep = 1
-        return PouchdbCrypto.DeleteCryptConfig(this.fastenDbService.current_user)
-          .then(() => {
-            //an error occurred while importing credential
-            const toastNotification = new ToastNotification()
-            toastNotification.type = ToastType.Error
-            toastNotification.message = "Provided encryption key does not match. Please try a different key"
-            toastNotification.autohide = false
-            this.toastService.show(toastNotification)
-          })
-      })
-  }
-
-
-  private readFileContent(file: File): Promise<string>{
-    return new Promise<string>((resolve, reject) => {
-      if (!file) {
-        resolve('');
-      }
-      const reader = new FileReader();
-      reader.onload = (e) => {
-        const text = reader.result.toString();
-        resolve(text);
-      };
-      reader.readAsText(file);
-    });
-  }
-}

frontend/src/app/pages/medical-history/medical-history.component.html

@@ -0,0 +1,124 @@
+<div class="az-content">
+  <div class="container">
+    <div class="az-content-body">
+
+      <!-- Header Row -->
+      <div class="row">
+        <div class="col-6 bg-indigo tx-white d-flex align-items-center">
+          <h1>Medical History</h1>
+        </div>
+        <div class="col-3 mt-2 mb-2 tx-12">
+          <p class="mb-0">
+            <strong>Patient:</strong> Caldwell, Ruben<br/>
+            <strong>Address:</strong> 123 B Street<br/>Gainsville, FL, 94153<br/>
+            <strong>Date of Birth:</strong> June 20, 1929<br/>
+            <strong>Phone:</strong> 415-343-2342<br/>
+            <strong>Email:</strong> myemail@gmail.com
+          </p>
+        </div>
+        <div class="col-3 tx-indigo mt-2 mb-2 tx-12">
+          <p class="mb-0">
+            <strong>Primary Care:</strong> Bishop, J. ANRP<br/>
+            <strong>Address:</strong> Malcom Randall VA <br/>Medical Center Gainsville FL<br/>
+            <strong>Phone:</strong> 123-321-5532<br/>
+            <strong>Email:</strong> myemail@va.com<br/>
+          </p>
+        </div>
+      </div>
+
+      <!-- Conditions Title -->
+      <div class="row mt-5 mb-3">
+        <div class="col-6">
+          <h1>Condition</h1>
+        </div>
+        <div class="col-6 tx-indigo">
+          <h1>History</h1>
+        </div>
+      </div>
+
+      <!-- Condition List -->
+
+      <div class="row bg-indigo tx-white pt-1 pb-1">
+        <!-- Condition Header -->
+        <div class="col-6 d-flex align-items-center">
+          <h3 class="mb-0">Gout</h3>
+        </div>
+        <div class="col-6 d-flex align-items-center">
+          <h3 class="mb-0">Nov 16, 2002 - Present</h3>
+        </div>
+      </div>
+
+
+      <div class="row">
+        <!-- Condition Details -->
+
+        <div class="col-6 mb-2">
+
+          <div class="row  pl-3">
+            <div class="col-12 mt-3 mb-2 tx-indigo">
+              <h5>Involved in Care</h5>
+            </div>
+
+            <div class="col-6">
+              <strong>James Bishop</strong>, ANRP
+            </div>
+            <div class="col-6">
+              Primary Care
+            </div>
+
+            <div class="col-6">
+              <strong>Matthew Leonard</strong>, MD
+            </div>
+            <div class="col-6">
+              Diagnosing Physician
+            </div>
+
+            <div class="col-6">
+              <strong>Stephanie Wrenn</strong>, MD
+            </div>
+            <div class="col-6">
+              Dietitian
+            </div>
+
+
+            <div class="col-12  mt-3 mb-2 tx-indigo">
+              <h5>Initial Presentation</h5>
+            </div>
+            <div class="col-12">
+              Acute right knee pain and tenderness around the joint line - this was likely caused by acute renal failure.
+            </div>
+          </div>
+
+
+
+        </div>
+        <div class="col-6 mb-2 bg-gray-100">
+          <div class="row">
+            <div class="col-12 mt-3 mb-2 tx-indigo">
+              <h5>Nov 19, 2012</h5>
+            </div>
+            <div class="col-12 mt-2 mb-2">
+              <strong>Medications:</strong> Colchicine, as needed for gout attacks
+            </div>
+
+
+            <div class="col-12 mt-3 mb-2 tx-indigo">
+              <h5>Nov 16, 2012</h5>
+            </div>
+            <div class="col-12 mt-2 mb-2">
+              <strong>Procedures:</strong> The fluid in your right knee was drained.
+            </div>
+            <div class="col-12 mt-2 mb-2">
+              <strong>Tests and Examinations:</strong> The fluid tested prositive for gout crystals
+            </div>
+            <div class="col-12 mt-2 mb-2">
+              <strong>Medications:</strong> You were given a steroid injection to reduce inflammation and as short course prednistone to reduce pain and inflammation
+            </div>
+          </div>
+        </div>
+      </div>
+
+
+    </div>
+  </div>
+</div>

frontend/src/app/pages/medical-history/medical-history.component.spec.ts

@@ -0,0 +1,23 @@
+import { ComponentFixture, TestBed } from '@angular/core/testing';
+
+import { MedicalHistoryComponent } from './medical-history.component';
+
+describe('MedicalHistoryComponent', () => {
+  let component: MedicalHistoryComponent;
+  let fixture: ComponentFixture<MedicalHistoryComponent>;
+
+  beforeEach(async () => {
+    await TestBed.configureTestingModule({
+      declarations: [ MedicalHistoryComponent ]
+    })
+    .compileComponents();
+
+    fixture = TestBed.createComponent(MedicalHistoryComponent);
+    component = fixture.componentInstance;
+    fixture.detectChanges();
+  });
+
+  it('should create', () => {
+    expect(component).toBeTruthy();
+  });
+});

frontend/src/app/pages/medical-history/medical-history.component.ts

@@ -0,0 +1,15 @@
+import { Component, OnInit } from '@angular/core';
+
+@Component({
+  selector: 'app-medical-history',
+  templateUrl: './medical-history.component.html',
+  styleUrls: ['./medical-history.component.scss']
+})
+export class MedicalHistoryComponent implements OnInit {
+
+  constructor() { }
+
+  ngOnInit(): void {
+  }
+
+}

frontend/src/app/pages/medical-sources/medical-sources.component.html

@@ -30,7 +30,7 @@
         <div *ngFor="let sourceInfo of connectedSourceList" class="col-sm-3 mg-b-20 px-3">
           <div class="card h-100 d-flex align-items-center justify-content-center p-3 rounded-0 cursor-pointer">
             <div (click)="openModal(contentModalRef, sourceInfo)" class="card-body">
-              <img [src]="'assets/sources/'+sourceInfo?.metadata['source_type']+'.png'" alt="client" class="img-fluid">
+              <img [src]="'assets/sources/'+sourceInfo?.metadata['source_type']+'.png'" [alt]="sourceInfo?.metadata.display" class="img-fluid">
               <div *ngIf="status[sourceInfo.source?.source_type]" class="progress">
                 <div [style.width]="status[sourceInfo?.source?.source_type] == 'authorize' ? '33%' : '66%'" class="bg-indigo progress-bar progress-bar-striped progress-bar-animated" role="progressbar"></div>
               </div>

frontend/src/app/pages/medical-sources/medical-sources.component.ts

@@ -1,20 +1,17 @@
 import {Component, OnInit} from '@angular/core';
 import {LighthouseService} from '../../services/lighthouse.service';
-import {FastenDbService} from '../../services/fasten-db.service';
-import {LighthouseSourceMetadata} from '../../../lib/models/lighthouse/lighthouse-source-metadata';
-import {Source} from '../../../lib/models/database/source';
+import {FastenApiService} from '../../services/fasten-api.service';
+import {LighthouseSourceMetadata} from '../../models/lighthouse/lighthouse-source-metadata';
+import {Source} from '../../models/fasten/source';
 import {getAccessTokenExpiration, jwtDecode} from 'fhirclient/lib/lib';
 import BrowserAdapter from 'fhirclient/lib/adapters/BrowserAdapter';
 import {MetadataSource} from '../../models/fasten/metadata-source';
 import {ModalDismissReasons, NgbModal} from '@ng-bootstrap/ng-bootstrap';
 import {ActivatedRoute, Router} from '@angular/router';
 import {Location} from '@angular/common';
-import {SourceType} from '../../../lib/models/database/source_types';
-import {QueueService} from '../../workers/queue.service';
 import {ToastService} from '../../services/toast.service';
 import {ToastNotification, ToastType} from '../../models/fasten/toast';
 import {SourceSyncMessage} from '../../models/queue/source-sync-message';
-import {UpsertSummary} from '../../../lib/models/fasten/upsert-summary';
 import {environment} from '../../../environments/environment';
 // If you dont import this angular will import the wrong "Location"
 
@@ -35,15 +32,15 @@ export class MedicalSourcesComponent implements OnInit {
 
   constructor(
     private lighthouseApi: LighthouseService,
-    private fastenDb: FastenDbService,
+    private fastenApi: FastenApiService,
     private modalService: NgbModal,
     private route: ActivatedRoute,
     private router: Router,
     private location: Location,
-    private queueService: QueueService,
     private toastService: ToastService
   ) { }
 
+
   environment_name = environment.environment_name
   status: { [name: string]: string } = {}
 
@@ -66,9 +63,9 @@ export class MedicalSourcesComponent implements OnInit {
         this.callback(callbackSourceType).then(console.log)
       }
 
-      this.fastenDb.GetSources()
-        .then((paginatedList) => {
-          const sourceList = paginatedList.rows as Source[]
+      this.fastenApi.getSources()
+        .subscribe((paginatedList: Source[]) => {
+          const sourceList = paginatedList as Source[]
 
           for (const sourceType in this.metadataSources) {
             let isConnected = false
@@ -167,7 +164,7 @@ export class MedicalSourcesComponent implements OnInit {
         //Create FHIR Client
 
         const dbSourceCredential = new Source({
-          source_type: sourceType as SourceType,
+          source_type: sourceType,
 
           authorization_endpoint: sourceMetadata.authorization_endpoint,
           token_endpoint: sourceMetadata.token_endpoint,
@@ -194,9 +191,44 @@ export class MedicalSourcesComponent implements OnInit {
           expires_at:            parseInt(getAccessTokenExpiration(payload, new BrowserAdapter())),
         })
 
-        await this.fastenDb.UpsertSource(dbSourceCredential).then(console.log)
-        this.queueSourceSyncWorker(sourceType as SourceType, dbSourceCredential)
+        this.fastenApi.createSource(dbSourceCredential)
+          .subscribe((msg) => {
+            // const sourceSyncMessage = JSON.parse(msg) as SourceSyncMessage
+            delete this.status[sourceType]
+            // window.location.reload();
 
+            console.log("source sync-all response:", msg)
+            //remove item from available sources list, add to connected sources.
+            this.availableSourceList.splice(this.availableSourceList.findIndex((item) => item.metadata.source_type == sourceType), 1);
+            if(this.connectedSourceList.findIndex((item) => item.metadata.source_type == sourceType) == -1){
+              //only add this as a connected source if its "new"
+              this.connectedSourceList.push({source: msg, metadata: this.metadataSources[sourceType]})
+            }
+
+            const toastNotification = new ToastNotification()
+            toastNotification.type = ToastType.Success
+            toastNotification.message = `Successfully connected ${sourceType}`
+
+            // const upsertSummary = sourceSyncMessage.response as UpsertSummary
+            // if(upsertSummary && upsertSummary.totalResources != upsertSummary.updatedResources.length){
+            //   toastNotification.message += `\n (total: ${upsertSummary.totalResources}, updated: ${upsertSummary.updatedResources.length})`
+            // } else if(upsertSummary){
+            //   toastNotification.message += `\n (total: ${upsertSummary.totalResources})`
+            // }
+
+            this.toastService.show(toastNotification)
+          },
+          (err) => {
+            delete this.status[sourceType]
+            // window.location.reload();
+
+            const toastNotification = new ToastNotification()
+            toastNotification.type = ToastType.Error
+            toastNotification.message = `An error occurred while accessing ${sourceType}: ${err}`
+            toastNotification.autohide = false
+            this.toastService.show(toastNotification)
+            console.error(err)
+          });
       })
   }
 
@@ -208,15 +240,15 @@ export class MedicalSourcesComponent implements OnInit {
   public uploadSourceBundleHandler(event) {
     this.uploadedFile = [event.addedFiles[0]]
     //TODO: handle manual bundles.
-    // this.fastenDb.CreateManualSource(event.addedFiles[0]).subscribe(
-    //   (respData) => {
-    //     console.log("source manual source create response:", respData)
-    //   },
-    //   (err) => {console.log(err)},
-    //   () => {
-    //     this.uploadedFile = []
-    //   }
-    // )
+    this.fastenApi.createManualSource(event.addedFiles[0]).subscribe(
+      (respData) => {
+        console.log("source manual source create response:", respData)
+      },
+      (err) => {console.log(err)},
+      () => {
+        this.uploadedFile = []
+      }
+    )
   }
 
   public openModal(contentModalRef, sourceListItem: SourceListItem) {
@@ -234,56 +266,22 @@ export class MedicalSourcesComponent implements OnInit {
     this.status[source.source_type] = "authorize"
     this.modalService.dismissAll()
 
-    this.queueSourceSyncWorker(source.source_type as SourceType, source)
+    this.fastenApi.syncSource(source.id).subscribe(
+      (respData) => {
+        delete this.status[source.source_type]
+        console.log("source sync response:", respData)
+      },
+      (err) => {
+        delete this.status[source.source_type]
+        console.log(err)
+      }
+    )
   }
 
 
   ///////////////////////////////////////////////////////////////////////////////////////
   // Private
   ///////////////////////////////////////////////////////////////////////////////////////
-  private queueSourceSyncWorker(sourceType: SourceType, source: Source){
-    //this work is pushed to the Sync Worker.
-    //TODO: if the user closes the browser the data update may not complete. we should set a status flag when "starting" sync, and then remove it when compelte
-    // so that we can show incompelte statuses
-    this.queueService.runSourceSyncWorker(source)
-      .subscribe((msg) => {
-          const sourceSyncMessage = JSON.parse(msg) as SourceSyncMessage
-          delete this.status[sourceType]
-          // window.location.reload();
-
-          console.log("source sync-all response:", sourceSyncMessage)
-          //remove item from available sources list, add to connected sources.
-          this.availableSourceList.splice(this.availableSourceList.findIndex((item) => item.metadata.source_type == sourceType), 1);
-          if(this.connectedSourceList.findIndex((item) => item.metadata.source_type == sourceType) == -1){
-            //only add this as a connected source if its "new"
-            this.connectedSourceList.push({source: sourceSyncMessage.source, metadata: this.metadataSources[sourceType]})
-          }
-
-          const toastNotification = new ToastNotification()
-          toastNotification.type = ToastType.Success
-          toastNotification.message = `Successfully connected ${sourceType}`
-
-          const upsertSummary = sourceSyncMessage.response as UpsertSummary
-          if(upsertSummary && upsertSummary.totalResources != upsertSummary.updatedResources.length){
-            toastNotification.message += `\n (total: ${upsertSummary.totalResources}, updated: ${upsertSummary.updatedResources.length})`
-          } else if(upsertSummary){
-            toastNotification.message += `\n (total: ${upsertSummary.totalResources})`
-          }
-
-          this.toastService.show(toastNotification)
-        },
-        (err) => {
-          delete this.status[sourceType]
-          // window.location.reload();
-
-          const toastNotification = new ToastNotification()
-          toastNotification.type = ToastType.Error
-          toastNotification.message = `An error occurred while accessing ${sourceType}: ${err}`
-          toastNotification.autohide = false
-          this.toastService.show(toastNotification)
-          console.error(err)
-        });
-  }
 
   private getDismissReason(reason: any): string {
     if (reason === ModalDismissReasons.ESC) {

frontend/src/app/pages/patient-profile/patient-profile.component.html

@@ -0,0 +1,191 @@
+<div class="az-content">
+  <div class="container">
+    <div class="az-content-body">
+
+      <!-- Header Row -->
+      <div class="row">
+        <div class="col-6 bg-indigo tx-white d-flex align-items-center">
+          <h1>Patient Profile</h1>
+        </div>
+        <div class="col-3 mt-2 mb-2 tx-12">
+          <p class="mb-0">
+            <strong>Patient:</strong> Caldwell, Ruben<br/>
+            <strong>Address:</strong> 123 B Street<br/>Gainsville, FL, 94153<br/>
+            <strong>Date of Birth:</strong> June 20, 1929<br/>
+            <strong>Phone:</strong> 415-343-2342<br/>
+            <strong>Email:</strong> myemail@gmail.com
+          </p>
+        </div>
+        <div class="col-3 tx-indigo mt-2 mb-2 tx-12">
+          <p class="mb-0">
+            <strong>Primary Care:</strong> Bishop, J. ANRP<br/>
+            <strong>Address:</strong> Malcom Randall VA <br/>Medical Center Gainsville FL<br/>
+            <strong>Phone:</strong> 123-321-5532<br/>
+            <strong>Email:</strong> myemail@va.com<br/>
+          </p>
+        </div>
+      </div>
+
+      <div class="pl-3 pr-3">
+        <!-- Patient Name Row -->
+        <div class="row mt-5 mb-3">
+          <div class="col-6">
+            <h1>Caldwell, Ruben</h1>
+          </div>
+        </div>
+
+        <!-- Patient Details -->
+        <div class="row">
+          <div class="col-6">
+            <h2 class="tx-indigo">Patient</h2>
+
+            <div class="row">
+              <div class="col-6">
+                <strong class="tx-indigo">First Name:</strong>
+              </div>
+              <div class="col-6">
+                Ruben
+              </div>
+
+              <div class="col-6">
+                <strong class="tx-indigo">Last Name:</strong>
+              </div>
+              <div class="col-6">
+                Caldwell
+              </div>
+
+              <div class="col-6">
+                <strong class="tx-indigo">Gender:</strong>
+              </div>
+              <div class="col-6">
+                M
+              </div>
+
+              <div class="col-6">
+                <strong class="tx-indigo">Martial Status:</strong>
+              </div>
+              <div class="col-6">
+                Married
+              </div>
+
+              <div class="col-6">
+                <strong class="tx-indigo">Religious Affil:</strong>
+              </div>
+              <div class="col-6">
+                N/A
+              </div>
+
+              <div class="col-6">
+                <strong class="tx-indigo">Ethnicity:</strong>
+              </div>
+              <div class="col-6">
+                White/Caucation
+              </div>
+
+              <div class="col-6">
+                <strong class="tx-indigo">Language:</strong>
+              </div>
+              <div class="col-6">
+                English
+              </div>
+
+              <div class="col-6">
+                <strong class="tx-indigo">Address:</strong>
+              </div>
+              <div class="col-6">
+                123 B Street<br/>Gainsville, FL, 94153<br/>
+              </div>
+
+              <div class="col-6">
+                <strong class="tx-indigo">Date of Birth:</strong>
+              </div>
+              <div class="col-6">
+                June 20, 1929
+              </div>
+
+              <div class="col-6">
+                <strong class="tx-indigo">Phone:</strong>
+              </div>
+              <div class="col-6">
+                415-343-2342
+              </div>
+
+              <div class="col-6">
+                <strong class="tx-indigo">Email:</strong>
+              </div>
+              <div class="col-6">
+                myemail@gmail.com
+              </div>
+
+            </div>
+
+          </div>
+          <div class="col-6">
+            <h2 class="tx-indigo">Care Provider</h2>
+
+            <div class="row">
+              <div class="col-6">
+                <strong class="tx-indigo">Primary Care:</strong>
+              </div>
+              <div class="col-6">
+                Bishop, J. ANRP
+              </div>
+
+              <div class="col-6">
+                <strong  class="tx-indigo">Address:</strong>
+              </div>
+              <div class="col-6">
+                Malcom Randall VA <br/>Medical Center Gainsville FL
+              </div>
+
+              <div class="col-6">
+                <strong  class="tx-indigo">Phone:</strong>
+              </div>
+              <div class="col-6">
+                123-321-5532
+              </div>
+
+              <div class="col-6">
+                <strong  class="tx-indigo">Email:</strong>
+              </div>
+              <div class="col-6">
+                myemail@va.com
+              </div>
+
+            </div>
+          </div>
+        </div>
+
+
+        <!-- Immunizations & Allergies -->
+        <div class="row mt-5">
+          <div class="col-6">
+            <h2 class="tx-indigo">Immunizations</h2>
+
+            <p>
+              <strong class="tx-indigo">Phenumovax</strong><br/>
+              07/09/2022<br/>
+              <br/>
+              <strong class="tx-indigo">Hepatitis B Series [complete]</strong><br/>
+              01/12/2005<br/>
+              <br/>
+              <strong class="tx-indigo">Tetanus Toxoid [complete]</strong><br/>
+              02/02/2010<br/>
+            </p>
+
+          </div>
+          <div class="col-6">
+            <h2 class="tx-indigo">Allergies</h2>
+
+            <p>
+              <strong class="tx-indigo">Latex</strong><br/>
+              (AV/Historical) with rash and agitation<br/>
+              <br/>
+
+            </p>
+          </div>
+        </div>
+      </div>
+    </div>
+  </div>
+</div>

frontend/src/app/pages/patient-profile/patient-profile.component.spec.ts

@@ -0,0 +1,23 @@
+import { ComponentFixture, TestBed } from '@angular/core/testing';
+
+import { PatientProfileComponent } from './patient-profile.component';
+
+describe('PatientProfileComponent', () => {
+  let component: PatientProfileComponent;
+  let fixture: ComponentFixture<PatientProfileComponent>;
+
+  beforeEach(async () => {
+    await TestBed.configureTestingModule({
+      declarations: [ PatientProfileComponent ]
+    })
+    .compileComponents();
+
+    fixture = TestBed.createComponent(PatientProfileComponent);
+    component = fixture.componentInstance;
+    fixture.detectChanges();
+  });
+
+  it('should create', () => {
+    expect(component).toBeTruthy();
+  });
+});

frontend/src/app/pages/patient-profile/patient-profile.component.ts

@@ -0,0 +1,15 @@
+import { Component, OnInit } from '@angular/core';
+
+@Component({
+  selector: 'app-patient-profile',
+  templateUrl: './patient-profile.component.html',
+  styleUrls: ['./patient-profile.component.scss']
+})
+export class PatientProfileComponent implements OnInit {
+
+  constructor() { }
+
+  ngOnInit(): void {
+  }
+
+}

frontend/src/app/pages/patient/patient.component.html

@@ -1,186 +0,0 @@
-
-<div class=" content">
-  <div class=" row">
-    <div class=" col-md-8">
-      <div class=" card">
-        <div class=" card-header"><h5 class=" title">Edit Profile</h5></div>
-        <div class=" card-body">
-          <form>
-            <div class=" row">
-              <div class=" col-md-5 pr-md-1">
-                <div class=" form-group">
-                  <label> Company (disabled) </label>
-                  <input
-                    class=" form-control"
-                    disabled=""
-                    placeholder="Company"
-                    type="text"
-                    value="Creative Code Inc."
-                  />
-                </div>
-              </div>
-              <div class=" col-md-3 px-md-1">
-                <div class=" form-group">
-                  <label> Username </label>
-                  <input
-                    class=" form-control"
-                    placeholder="Username"
-                    type="text"
-                    value="michael23"
-                  />
-                </div>
-              </div>
-              <div class=" col-md-4 pl-md-1">
-                <div class=" form-group">
-                  <label for="exampleInputEmail1"> Email address </label>
-                  <input
-                    class=" form-control"
-                    placeholder="mike@email.com"
-                    type="email"
-                  />
-                </div>
-              </div>
-            </div>
-            <div class=" row">
-              <div class=" col-md-6 pr-md-1">
-                <div class=" form-group">
-                  <label> First Name </label>
-                  <input
-                    class=" form-control"
-                    placeholder="Company"
-                    type="text"
-                    value="Mike"
-                  />
-                </div>
-              </div>
-              <div class=" col-md-6 pl-md-1">
-                <div class=" form-group">
-                  <label> Last Name </label>
-                  <input
-                    class=" form-control"
-                    placeholder="Last Name"
-                    type="text"
-                    value="Andrew"
-                  />
-                </div>
-              </div>
-            </div>
-            <div class=" row">
-              <div class=" col-md-12">
-                <div class=" form-group">
-                  <label> Address </label>
-                  <input
-                    class=" form-control"
-                    placeholder="Home Address"
-                    type="text"
-                    value="Bld Mihail Kogalniceanu, nr. 8 Bl 1, Sc 1, Ap 09"
-                  />
-                </div>
-              </div>
-            </div>
-            <div class=" row">
-              <div class=" col-md-4 pr-md-1">
-                <div class=" form-group">
-                  <label> City </label>
-                  <input
-                    class=" form-control"
-                    placeholder="City"
-                    type="text"
-                    value="Mike"
-                  />
-                </div>
-              </div>
-              <div class=" col-md-4 px-md-1">
-                <div class=" form-group">
-                  <label> Country </label>
-                  <input
-                    class=" form-control"
-                    placeholder="Country"
-                    type="text"
-                    value="Andrew"
-                  />
-                </div>
-              </div>
-              <div class=" col-md-4 pl-md-1">
-                <div class=" form-group">
-                  <label> Postal Code </label>
-                  <input
-                    class=" form-control"
-                    placeholder="ZIP Code"
-                    type="number"
-                  />
-                </div>
-              </div>
-            </div>
-            <div class=" row">
-              <div class=" col-md-8">
-                <div class=" form-group">
-                  <label> About Me </label>
-                  <textarea
-                    class=" form-control"
-                    cols="80"
-                    placeholder="Here can be your description"
-                    rows="4"
-                    value="Mike"
-                  >
-Lamborghini Mercy, Your chick she so thirsty, I'm in that two seat Lambo.
-</textarea
-                  >
-                </div>
-              </div>
-            </div>
-          </form>
-        </div>
-        <div class=" card-footer">
-          <button class=" btn btn-fill btn-danger" type="submit">Save</button>
-        </div>
-      </div>
-    </div>
-    <div class=" col-md-4">
-      <div class=" card card-user">
-        <div class=" card-body">
-          <p class=" card-text"></p>
-          <div class=" author">
-            <div class=" block block-one"></div>
-            <div class=" block block-two"></div>
-            <div class=" block block-three"></div>
-            <div class=" block block-four"></div>
-            <a href="javascript:void(0)">
-              <img alt="..." class=" avatar" src="assets/img/emilyz.jpg" />
-
-              <h5 class=" title">Mike Andrew</h5>
-            </a>
-            <p class=" description">Ceo/Co-Founder</p>
-          </div>
-          <div class=" card-description">
-            Do not be scared of the truth because we need to restart the human
-            foundation in truth And I love you like Kanye loves Kanye I love
-            Rick Owens’€™ bed design but the back is...
-          </div>
-        </div>
-        <div class=" card-footer">
-          <div class=" button-container">
-            <button
-              class=" btn btn-icon btn-round btn-facebook"
-              href="javascript:void(0)"
-            >
-              <i class=" fab fa-facebook"> </i>
-            </button>
-            <button
-              class=" btn btn-icon btn-round btn-twitter"
-              href="javascript:void(0)"
-            >
-              <i class=" fab fa-twitter"> </i>
-            </button>
-            <button
-              class=" btn btn-icon btn-round btn-google"
-              href="javascript:void(0)"
-            >
-              <i class=" fab fa-google-plus"> </i>
-            </button>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>

frontend/src/app/pages/patient/patient.component.ts

@@ -1,11 +0,0 @@
-import { Component, OnInit } from "@angular/core";
-
-@Component({
-  selector: "app-patient",
-  templateUrl: "patient.component.html"
-})
-export class PatientComponent implements OnInit {
-  constructor() {}
-
-  ngOnInit() {}
-}

frontend/src/app/pages/resource-detail/resource-detail.component.ts

@@ -1,8 +1,7 @@
 import { Component, OnInit } from '@angular/core';
-import {FastenDbService} from '../../services/fasten-db.service';
+import {FastenApiService} from '../../services/fasten-api.service';
 import {ActivatedRoute, Router} from '@angular/router';
-import {ResourceFhir} from '../../../lib/models/database/resource_fhir';
-import {Base64} from '../../../lib/utils/base64';
+import {ResourceFhir} from '../../models/fasten/resource_fhir';
 
 @Component({
   selector: 'app-resource-detail',
@@ -14,23 +13,16 @@ export class ResourceDetailComponent implements OnInit {
   sourceName: string = ""
   resource: ResourceFhir = null
 
-  constructor(private fastenDb: FastenDbService, private router: Router, private route: ActivatedRoute) {
+  constructor(private fastenApi: FastenApiService, private router: Router, private route: ActivatedRoute) {
   }
 
   ngOnInit(): void {
-    //always request the resource by id
-    let resourceId = Base64.Decode(this.route.snapshot.paramMap.get('resource_id'))
-    if (resourceId){
-      this.fastenDb.GetResource(resourceId)
-        .then((resourceFhir) => {
+    this.fastenApi.getResourceBySourceId(this.route.snapshot.paramMap.get('source_id'), this.route.snapshot.paramMap.get('resource_id')).subscribe((resourceFhir) => {
+      console.log("RESOURECE FHIR", resourceFhir)
       this.resource = resourceFhir;
+      this.sourceId = this.route.snapshot.paramMap.get('source_id')
+      this.sourceName = "unknown" //TODO popualte this
     });
-      this.sourceId = resourceId.split(":")[1]
-      this.sourceName = Base64.Decode(this.sourceId).split(":")[1]
-    } else {
-      console.log("invalid or missing resource id")
-    }
-
   }
 
 }

frontend/src/app/pages/source-detail/source-detail.component.html

@@ -18,7 +18,7 @@
               <div class="patient-row row">
                 <div class="col-7 patient-name"><h3 class="pull-left text-primary">{{getPatientName()}}</h3></div>
                 <div class="col-5">
-                  <a routerLink="/resource/{{selectedPatient?.base64Id()}}" class="btn btn-indigo btn-icon float-right">
+                  <a routerLink="/source/{{selectedSource?.id}}/resource/{{selectedPatient?.source_resource_id}}" class="btn btn-indigo btn-icon float-right">
                     <i class="fas fa-info-circle"></i>
                   </a>
                 </div>

frontend/src/app/pages/source-detail/source-detail.component.ts

@@ -1,11 +1,9 @@
 import {Component, OnInit, ViewChild} from '@angular/core';
 import {ActivatedRoute, Router} from '@angular/router';
-import {Source} from '../../../lib/models/database/source';
-import {FastenDbService} from '../../services/fasten-db.service';
-import {ResourceFhir} from '../../../lib/models/database/resource_fhir';
+import {Source} from '../../models/fasten/source';
+import {FastenApiService} from '../../services/fasten-api.service';
+import {ResourceFhir} from '../../models/fasten/resource_fhir';
 import {getPath} from '../../components/list-generic-resource/utils';
-import {Base64} from '../../../lib/utils/base64';
-
 
 @Component({
   selector: 'app-source-detail',
@@ -20,7 +18,7 @@ export class SourceDetailComponent implements OnInit {
 
   resourceTypeCounts: { [name: string]: number } = {}
 
-  constructor(private fastenDb: FastenDbService, private router: Router, private route: ActivatedRoute) {
+  constructor(private fastenApi: FastenApiService, private router: Router, private route: ActivatedRoute) {
     //check if the current Source was sent over using the router state storage:
     if(this.router.getCurrentNavigation()?.extras?.state){
       this.selectedSource = this.router.getCurrentNavigation().extras.state as Source
@@ -29,7 +27,7 @@ export class SourceDetailComponent implements OnInit {
 
   ngOnInit(): void {
     //always request the source summary
-    this.fastenDb.GetSourceSummary(Base64.Decode(this.route.snapshot.paramMap.get('source_id'))).then((sourceSummary) => {
+    this.fastenApi.getSourceSummary(this.route.snapshot.paramMap.get('source_id')).subscribe((sourceSummary) => {
       this.selectedSource = sourceSummary.source;
       this.selectedPatient = sourceSummary.patient;
       for(let resourceTypeCount of sourceSummary.resource_type_counts){

frontend/src/app/services/auth-interceptor.service.ts

@@ -1,6 +1,5 @@
 import { Injectable, Injector } from '@angular/core';
 import {HttpErrorResponse, HttpEvent, HttpHandler, HttpInterceptor, HttpRequest} from '@angular/common/http';
-import { FastenDbService } from './fasten-db.service';
 import {Router} from '@angular/router';
 import {Observable, of, throwError} from 'rxjs';
 import {catchError} from 'rxjs/operators';
@@ -30,40 +29,61 @@ export class AuthInterceptorService implements HttpInterceptor {
   }
 
   intercept(req: HttpRequest<any>, next: HttpHandler): Observable<HttpEvent<any>> {
-    let authToken = this.authService.GetAuthToken()
-    if(!authToken){
-      //no authToken available, lets just handle the request as-is
-      return next.handle(req)
-    }
 
-    //only intercept requests to the Fasten API, Database & Lighthouse, all other requests should be sent as-is
+    console.log("Intercepting Request", req)
+
+    //only intercept requests to the fasten API & lighthouse, all other requests should be sent as-is
     let reqUrl = new URL(req.url)
     let lighthouseUrl = new URL(GetEndpointAbsolutePath(globalThis.location, environment.lighthouse_api_endpoint_base))
     let apiUrl = new URL(GetEndpointAbsolutePath(globalThis.location, environment.fasten_api_endpoint_base))
 
-    //skip database, header is sent automatically via PouchDB
-    // let databaseUrl = new URL(GetEndpointAbsolutePath(globalThis.location, environment.couchdb_endpoint_base))
-
     if(
-      (reqUrl.origin == lighthouseUrl.origin && reqUrl.pathname.startsWith(lighthouseUrl.pathname))
+      !((reqUrl.origin == apiUrl.origin && reqUrl.pathname.startsWith(apiUrl.pathname)) ||
+        (reqUrl.origin == lighthouseUrl.origin && reqUrl.pathname.startsWith(lighthouseUrl.pathname)))
     ){
-      //all requests to the lighthouse require the JWT
-      console.log("making authorized request...")
-      // Clone the request to add the new auth header.
+      return next.handle(req)
+    }
+
+    // Clone the request to add the new header.
     const authReq = req.clone({headers: req.headers.set('Authorization', 'Bearer ' + this.authService.GetAuthToken())});
     // catch the error, make specific functions for catching specific errors and you can chain through them with more catch operators
     return next.handle(authReq).pipe(catchError(x=> this.handleAuthError(x))); //here use an arrow function, otherwise you may get "Cannot read property 'navigate' of undefined" on angular 4.4.2/net core 2/webpack 2.70
-    }
-    // else if(){
-    //   //TODO: only CORS requests to the API endpoint require JWT, but they also require a custom header.
-    //
-    //   //(reqUrl.origin == lighthouseUrl.origin && reqUrl.pathname.startsWith(lighthouseUrl.pathname)) ||
-    //   //       () ||
-    //   //       (reqUrl.origin == apiUrl.origin && reqUrl.pathname.startsWith(apiUrl.pathname))
-    //
-    // }
 
-    return next.handle(req)
+
+    // let authToken = this.authService.GetAuthToken()
+    // if(!authToken){
+    //   //no authToken available, lets just handle the request as-is
+    //   return next.handle(req)
+    // }
+    //
+    // //only intercept requests to the Fasten API, Database & Lighthouse, all other requests should be sent as-is
+    // let reqUrl = new URL(req.url)
+    // let lighthouseUrl = new URL(GetEndpointAbsolutePath(globalThis.location, environment.lighthouse_api_endpoint_base))
+    // let apiUrl = new URL(GetEndpointAbsolutePath(globalThis.location, environment.fasten_api_endpoint_base))
+    //
+    // //skip database, header is sent automatically via PouchDB
+    // // let databaseUrl = new URL(GetEndpointAbsolutePath(globalThis.location, environment.couchdb_endpoint_base))
+    //
+    // if(
+    //   (reqUrl.origin == lighthouseUrl.origin && reqUrl.pathname.startsWith(lighthouseUrl.pathname))
+    // ){
+    //   //all requests to the lighthouse require the JWT
+    //   console.log("making authorized request...")
+    //   // Clone the request to add the new auth header.
+    //   const authReq = req.clone({headers: req.headers.set('Authorization', 'Bearer ' + this.authService.GetAuthToken())});
+    //   // catch the error, make specific functions for catching specific errors and you can chain through them with more catch operators
+    //   return next.handle(authReq).pipe(catchError(x=> this.handleAuthError(x))); //here use an arrow function, otherwise you may get "Cannot read property 'navigate' of undefined" on angular 4.4.2/net core 2/webpack 2.70
+    // }
+    // // else if(){
+    // //   //TODO: only CORS requests to the API endpoint require JWT, but they also require a custom header.
+    // //
+    // //   //(reqUrl.origin == lighthouseUrl.origin && reqUrl.pathname.startsWith(lighthouseUrl.pathname)) ||
+    // //   //       () ||
+    // //   //       (reqUrl.origin == apiUrl.origin && reqUrl.pathname.startsWith(apiUrl.pathname))
+    // //
+    // // }
+    //
+    // return next.handle(req)
 
   }
 }

frontend/src/app/services/auth.service.ts

@@ -1,13 +1,11 @@
 import { Injectable } from '@angular/core';
 import {HttpClient, HttpHeaders} from '@angular/common/http';
-import {FastenDbService} from './fasten-db.service';
-import {User} from '../../lib/models/fasten/user';
+import {User} from '../models/fasten/user';
 import {environment} from '../../environments/environment';
 import {GetEndpointAbsolutePath} from '../../lib/utils/endpoint_absolute_path';
 import {ResponseWrapper} from '../models/response-wrapper';
 import * as Oauth from '@panva/oauth4webapi';
 import {SourceState} from '../models/fasten/source-state';
-import {Session} from '../models/database/session';
 import * as jose from 'jose';
 import {UserRegisteredClaims} from '../models/fasten/user-registered-claims';
 
@@ -137,25 +135,29 @@ export class AuthService {
     if(!hasAuthToken){
       return false
     }
-    //check if the authToken works
-    let databaseEndpointBase = GetEndpointAbsolutePath(globalThis.location, environment.couchdb_endpoint_base)
-    try {
-      let resp = await this._httpClient.get<any>(`${databaseEndpointBase}/_session`, {
-        headers: new HttpHeaders({
-          'Content-Type':  'application/json',
-          Authorization: `Bearer ${authToken}`
-        })
-      }).toPromise()
-      //  logic to check if user is logged in here.
-      let session = resp as Session
-      if(!session.ok || session?.info?.authenticated != "jwt" || !session.userCtx?.name){
-        //invalid session, not jwt auth, or username is empty
-        return false
-      }
+
+    //todo: check if the authToken has expired
     return true
-    } catch (e) {
-      return false
-    }
+
+    // //check if the authToken has expired.
+    // let databaseEndpointBase = GetEndpointAbsolutePath(globalThis.location, environment.couchdb_endpoint_base)
+    // try {
+    //   let resp = await this._httpClient.get<any>(`${databaseEndpointBase}/_session`, {
+    //     headers: new HttpHeaders({
+    //       'Content-Type':  'application/json',
+    //       Authorization: `Bearer ${authToken}`
+    //     })
+    //   }).toPromise()
+    //   //  logic to check if user is logged in here.
+    //   let session = resp as Session
+    //   if(!session.ok || session?.info?.authenticated != "jwt" || !session.userCtx?.name){
+    //     //invalid session, not jwt auth, or username is empty
+    //     return false
+    //   }
+    //   return true
+    // } catch (e) {
+    //   return false
+    // }
   }
 
   public GetAuthToken(): string {

frontend/src/app/services/fasten-api.service.spec.ts

@@ -1,16 +1,16 @@
 import { TestBed } from '@angular/core/testing';
 
-import { FastenDbService } from './fasten-db.service';
+import { FastenApiService } from './fasten-api.service';
 import {HttpClientTestingModule} from '@angular/common/http/testing';
 
-describe('FastenDbService', () => {
-  let service: FastenDbService;
+describe('FastenApiService', () => {
+  let service: FastenApiService;
 
   beforeEach(() => {
     TestBed.configureTestingModule({
       imports: [HttpClientTestingModule],
     });
-    service = TestBed.inject(FastenDbService);
+    service = TestBed.inject(FastenApiService);
   });
 
   it('should be created', () => {

frontend/src/app/services/fasten-api.service.ts

@@ -0,0 +1,131 @@
+import { Injectable } from '@angular/core';
+import { HttpClient, HttpHeaders } from '@angular/common/http';
+import {Observable} from 'rxjs';
+import { Router } from '@angular/router';
+import {map} from 'rxjs/operators';
+import {ResponseWrapper} from '../models/response-wrapper';
+import {Source} from '../models/fasten/source';
+import {User} from '../models/fasten/user';
+import {ResourceFhir} from '../models/fasten/resource_fhir';
+import {SourceSummary} from '../models/fasten/source-summary';
+import {Summary} from '../models/fasten/summary';
+import {MetadataSource} from '../models/fasten/metadata-source';
+import {AuthService} from './auth.service';
+import {GetEndpointAbsolutePath} from '../../lib/utils/endpoint_absolute_path';
+import {environment} from '../../environments/environment';
+
+@Injectable({
+  providedIn: 'root'
+})
+export class FastenApiService {
+
+  constructor(private _httpClient: HttpClient,  private router: Router, private authService: AuthService) {
+  }
+
+
+  /*
+  SECURE ENDPOINTS
+  */
+  getSummary(): Observable<Summary> {
+    return this._httpClient.get<any>(`${GetEndpointAbsolutePath(globalThis.location, environment.fasten_api_endpoint_base)}/secure/summary`, )
+      .pipe(
+        map((response: ResponseWrapper) => {
+          console.log("Summary RESPONSE", response)
+          return response.data as Summary
+        })
+      );
+  }
+
+  createSource(source: Source): Observable<Source> {
+    return this._httpClient.post<any>(`${GetEndpointAbsolutePath(globalThis.location, environment.fasten_api_endpoint_base)}/secure/source`, source)
+      .pipe(
+        map((response: ResponseWrapper) => {
+          console.log("SOURCE RESPONSE", response)
+          return response.data as Source
+        })
+      );
+  }
+
+  createManualSource(file: File): Observable<Source> {
+
+    const formData = new FormData();
+    formData.append('file', file);
+
+    return this._httpClient.post<any>(`${GetEndpointAbsolutePath(globalThis.location, environment.fasten_api_endpoint_base)}/secure/source/manual`, formData)
+      .pipe(
+        map((response: ResponseWrapper) => {
+          console.log("MANUAL SOURCE RESPONSE", response)
+          return response.data as Source
+        })
+      );
+  }
+
+  getSources(): Observable<Source[]> {
+    return this._httpClient.get<any>(`${GetEndpointAbsolutePath(globalThis.location, environment.fasten_api_endpoint_base)}/secure/source`)
+      .pipe(
+        map((response: ResponseWrapper) => {
+          console.log("SOURCE RESPONSE", response)
+          return response.data as Source[]
+        })
+      );
+  }
+
+  getSource(sourceId: string): Observable<Source> {
+    return this._httpClient.get<any>(`${GetEndpointAbsolutePath(globalThis.location, environment.fasten_api_endpoint_base)}/secure/source/${sourceId}`)
+      .pipe(
+        map((response: ResponseWrapper) => {
+          console.log("SOURCE RESPONSE", response)
+          return response.data as Source
+        })
+      );
+  }
+
+  getSourceSummary(sourceId: string): Observable<SourceSummary> {
+    return this._httpClient.get<any>(`${GetEndpointAbsolutePath(globalThis.location, environment.fasten_api_endpoint_base)}/secure/source/${sourceId}/summary`)
+      .pipe(
+        map((response: ResponseWrapper) => {
+          console.log("SOURCE RESPONSE", response)
+          return response.data as SourceSummary
+        })
+      );
+  }
+
+  syncSource(sourceId: string): Observable<any> {
+    return this._httpClient.post<any>(`${GetEndpointAbsolutePath(globalThis.location, environment.fasten_api_endpoint_base)}/secure/source/${sourceId}/sync`, {})
+      .pipe(
+        map((response: ResponseWrapper) => {
+          console.log("SOURCE RESPONSE", response)
+          return response.data
+        })
+      );
+  }
+
+  getResources(sourceResourceType?: string, sourceID?: string): Observable<ResourceFhir[]> {
+    let queryParams = {}
+    if(sourceResourceType){
+      queryParams["sourceResourceType"] = sourceResourceType
+    }
+    if(sourceID){
+      queryParams["sourceID"] = sourceID
+    }
+
+    return this._httpClient.get<any>(`${GetEndpointAbsolutePath(globalThis.location, environment.fasten_api_endpoint_base)}/secure/resource/fhir`, {params: queryParams})
+      .pipe(
+        map((response: ResponseWrapper) => {
+          console.log("RESPONSE", response)
+          return response.data as ResourceFhir[]
+        })
+      );
+  }
+
+  getResourceBySourceId(sourceId: string, resourceId: string): Observable<ResourceFhir> {
+
+    return this._httpClient.get<any>(`${GetEndpointAbsolutePath(globalThis.location, environment.fasten_api_endpoint_base)}/secure/resource/fhir/${sourceId}/${resourceId}`)
+      .pipe(
+        map((response: ResponseWrapper) => {
+          console.log("RESPONSE", response)
+          return response.data as ResourceFhir
+        })
+      );
+  }
+}

frontend/src/app/services/fasten-db.service.ts

@@ -1,147 +0,0 @@
-import { Injectable } from '@angular/core';
-import {PouchdbRepository} from '../../lib/database/pouchdb_repository';
-import {User} from '../../lib/models/fasten/user';
-import {ResponseWrapper} from '../models/response-wrapper';
-import {HttpClient} from '@angular/common/http';
-import {Summary} from '../../lib/models/fasten/summary';
-import {DocType} from '../../lib/database/constants';
-import {ResourceTypeCounts} from '../../lib/models/fasten/source-summary';
-import {Base64} from '../../lib/utils/base64';
-import * as jose from 'jose'
-
-// PouchDB & plugins (must be similar to the plugins specified in pouchdb repository)
-import * as PouchDB from 'pouchdb/dist/pouchdb';
-import find from 'pouchdb-find';
-PouchDB.plugin(find); //does not work in
-import * as PouchUpsert from 'pouchdb-upsert';
-PouchDB.plugin(PouchUpsert);
-import * as PouchCrypto from 'crypto-pouch';
-PouchDB.plugin(PouchCrypto);
-import PouchAuth from 'pouchdb-authentication'
-import {PouchdbCrypto} from '../../lib/database/plugins/crypto';
-import {environment} from '../../environments/environment';
-import {GetEndpointAbsolutePath} from '../../lib/utils/endpoint_absolute_path';
-import {AuthService} from './auth.service';
-PouchDB.plugin(PouchAuth);
-
-@Injectable({
-  providedIn: 'root'
-})
-export class FastenDbService extends PouchdbRepository {
-
-
-  // There are 3 different ways to initialize the Database
-  // - explicitly after signin/signup
-  // - explicitly during web-worker init (not supported by this class, see PouchdbRepository.NewPouchdbRepositoryWebWorker)
-  // - implicitly after Lighthouse redirect (when user is directed back to the app)
-  // Three peices of information are required during intialization
-  // - couchdb endpoint (constant, see environment.couchdb_endpoint_base)
-  // - username
-  // - JWT token
-  constructor(private _httpClient: HttpClient, private authService: AuthService) {
-    super(environment.couchdb_endpoint_base);
-  }
-
-
-  /**
-   * Try to get PouchDB database using token auth information
-   * This method must handle 2 types of authentication
-   * - pouchdb init after signin/signup
-   * - implicit init after lighthouse redirect
-   * @constructor
-   */
-  public override async GetSessionDB(): Promise<PouchDB.Database>  {
-    if(this.pouchDb){
-      console.log("Session DB already exists..")
-      return this.pouchDb
-    }
-
-    //check if we have a JWT token (we should, otherwise the auth-guard would have redirected to login page)
-    let authToken = this.authService.GetAuthToken()
-    if(!authToken){
-      throw new Error("no auth token found")
-    }
-
-    //parse the authToken to get user information
-    this.current_user = this.authService.GetCurrentUser().sub
-
-    // add JWT bearer token header to all requests
-    // https://stackoverflow.com/questions/62129654/how-to-handle-jwt-authentication-with-rxdb
-    this.pouchDb = new PouchDB(this.getRemoteUserDb(this.current_user), {
-      fetch: function (url, opts) {
-        opts.headers.set('Authorization', `Bearer ${authToken}`)
-        return PouchDB.fetch(url, opts);
-      }
-    })
-    return this.pouchDb
-  }
-
-  /**
-   * Is the crypto configuration for the authenticated user already available in the browser? Or do we need to import/generate new config.
-   */
-  public async isCryptConfigAvailable(): Promise<boolean>{
-    try {
-      await this.GetSessionDB()
-      let cryptConfig = await PouchdbCrypto.RetrieveCryptConfig(this.current_user)
-
-      return !!cryptConfig
-    }catch(e){
-      return false
-    }
-  }
-
-
-  public Close(): Promise<void> {
-    return super.Close()
-  }
-
-  ///////////////////////////////////////////////////////////////////////////////////////
-  // Summary
-
-  public async GetSummary(): Promise<Summary> {
-    const summary = new Summary()
-    summary.sources = await this.GetSources()
-      .then((paginatedResp) => paginatedResp.rows)
-
-    // summary.patients = []
-    summary.patients = await this.GetDB()
-      .then((db) => {
-
-        return db.find({
-          selector: {
-            doc_type: DocType.ResourceFhir,
-            source_resource_type: "Patient",
-          }
-        }).then((results) => {
-            return Promise.all((results.docs || []).map((doc) => PouchdbCrypto.decryptDocument(db, doc)))
-          })
-      })
-
-
-    summary.resource_type_counts = await this.findDocumentByPrefix(`${DocType.ResourceFhir}`, false)
-      .then((paginatedResp) => {
-        const lookup: {[name: string]: ResourceTypeCounts} = {}
-        paginatedResp?.rows.forEach((resourceWrapper) => {
-          const resourceIdParts = resourceWrapper.id.split(':')
-          const resourceType = resourceIdParts[2]
-
-          let currentResourceStats = lookup[resourceType] || {
-            count: 0,
-            source_id: Base64.Decode(resourceIdParts[1]),
-            resource_type: resourceType
-          }
-          currentResourceStats.count += 1
-          lookup[resourceType] = currentResourceStats
-        })
-
-        const arr = []
-        for(let key in lookup){
-          arr.push(lookup[key])
-        }
-        return arr
-      })
-
-
-    return summary
-  }
-}

frontend/src/app/services/lighthouse.service.ts

@@ -4,7 +4,7 @@ import {Observable} from 'rxjs';
 import {environment} from '../../environments/environment';
 import {map, tap} from 'rxjs/operators';
 import {ResponseWrapper} from '../models/response-wrapper';
-import {LighthouseSourceMetadata} from '../../lib/models/lighthouse/lighthouse-source-metadata';
+import {LighthouseSourceMetadata} from '../models/lighthouse/lighthouse-source-metadata';
 import * as Oauth from '@panva/oauth4webapi';
 import {SourceState} from '../models/fasten/source-state';
 import {MetadataSource} from '../models/fasten/metadata-source';

frontend/src/app/workers/queue.service.spec.ts

@@ -1,19 +0,0 @@
-import { TestBed } from '@angular/core/testing';
-
-import { QueueService } from './queue.service';
-import {HttpClientTestingModule} from '@angular/common/http/testing';
-
-describe('QueueService', () => {
-  let service: QueueService;
-
-  beforeEach(() => {
-    TestBed.configureTestingModule({
-      imports: [HttpClientTestingModule],
-    });
-    service = TestBed.inject(QueueService);
-  });
-
-  it('should be created', () => {
-    expect(service).toBeTruthy();
-  });
-});

frontend/src/app/workers/queue.service.ts

@@ -1,45 +0,0 @@
-import {Injectable} from '@angular/core';
-import {Observable, of} from 'rxjs';
-import {fromWorker} from 'observable-webworker';
-import {Source} from '../../lib/models/database/source';
-import {SourceSyncMessage} from '../models/queue/source-sync-message';
-import {ToastService} from '../services/toast.service';
-import {ToastNotification, ToastType} from '../models/fasten/toast';
-import {FastenDbService} from '../services/fasten-db.service';
-import {environment} from '../../environments/environment';
-import {AuthService} from '../services/auth.service';
-
-@Injectable({
-  providedIn: 'root'
-})
-export class QueueService {
-
-  constructor(private toastService: ToastService, private authService: AuthService) { }
-
-  runSourceSyncWorker(source: Source):Observable<string> {
-    if (typeof Worker !== 'undefined') {
-      const sourceSync = new SourceSyncMessage()
-      sourceSync.source = source
-      sourceSync.current_user = this.authService.GetCurrentUser().sub
-      sourceSync.auth_token = this.authService.GetAuthToken()
-      sourceSync.couchdb_endpoint_base = environment.couchdb_endpoint_base
-      sourceSync.fasten_api_endpoint_base = environment.fasten_api_endpoint_base
-      const input$: Observable<string> = of(JSON.stringify(sourceSync));
-      return fromWorker<string, string>(() => new Worker(new URL('./source-sync.worker', import.meta.url), {type: 'module'}), input$)
-        // .subscribe(message => {
-        //   console.log(`Got message`, message);
-        // });
-    }else {
-      // Web workers are not supported in this environment.
-      // You should add a fallback so that your program still executes correctly.
-      console.error("WORKERS ARE NOT SUPPORTED")
-
-      const toastNotificaiton = new ToastNotification()
-      toastNotificaiton.type = ToastType.Error
-      toastNotificaiton.message = "Your browser does not support web-workers. Cannot continue."
-      toastNotificaiton.autohide = false
-      this.toastService.show(toastNotificaiton)
-    }
-
-  }
-}

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

@@ -1,71 +0,0 @@
-/// <reference lib="webworker" />
-
-import {DoWork, runWorker} from 'observable-webworker';
-import {Observable} from 'rxjs';
-import {mergeMap} from 'rxjs/operators';
-import {SourceSyncMessage} from '../models/queue/source-sync-message';
-import {NewPouchdbRepositoryWebWorker, PouchdbRepository} from '../../lib/database/pouchdb_repository';
-import {NewClient} from '../../lib/conduit/factory';
-import {Source} from '../../lib/models/database/source';
-import {ClientConfig} from '../../lib/models/client/client-config';
-import {client} from 'fhirclient';
-
-export class SourceSyncWorker implements DoWork<string, string> {
-  public work(input$: Observable<string>): Observable<string> {
-    return input$.pipe(
-      //mergeMap allows us to convert a promise into an observable
-      // https://stackoverflow.com/questions/53649294/how-to-handle-for-promise-inside-a-piped-map
-      mergeMap(msg => {
-        try {
-          console.log(msg); // outputs 'Hello from main thread'
-          const sourceSyncMessage = JSON.parse(msg) as SourceSyncMessage
-
-          const db = NewPouchdbRepositoryWebWorker({current_user: sourceSyncMessage.current_user, auth_token: sourceSyncMessage.auth_token}, sourceSyncMessage.couchdb_endpoint_base)
-
-          let clientConfig = new ClientConfig()
-          clientConfig.fasten_api_endpoint_base = sourceSyncMessage.fasten_api_endpoint_base
-          const client = NewClient(sourceSyncMessage.source.source_type, new Source(sourceSyncMessage.source), clientConfig)
-          //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.UpsertSource()
-
-
-          //lets refresh the source information if required.
-          console.log("!!!!!!!!!!!!!!STARTING WORKER SYNC!!!!!!!!!", sourceSyncMessage)
-          return client.RefreshSourceToken()
-            .then((wasSourceRefreshed) => {
-              if(wasSourceRefreshed){
-                //the source was updated, we need to save the updated source information
-                return db.UpsertSource(client.source)
-                  .then(() => {
-                    return client
-                  })
-              }
-              return client
-            })
-            .then((client) => {
-              return client.SyncAll(db)
-            })
-            .then((resp) => {
-              console.log("!!!!!!!!!!!!!COMPLETE WORKER SYNC!!!!!!!!!!", resp)
-              sourceSyncMessage.response = resp
-              return JSON.stringify(sourceSyncMessage)
-
-            })
-            .catch((err) => {
-              console.error("!!!!!!!!!!!!!ERROR WORKER SYNC!!!!!!!!!!", err)
-              throw err
-            })
-          // return from(resp)
-
-        } catch (e) {
-          console.log("CAUGHT ERROR", e)
-          console.trace(e)
-          throw e
-        }
-      }),
-    );
-  }
-}
-
-runWorker(SourceSyncWorker);

frontend/src/lib/conduit/factory.ts

@@ -1,84 +0,0 @@
-import {SourceType} from '../models/database/source_types';
-import {Source} from '../models/database/source';
-import {IClient} from './interface';
-
-import {HealthITClient} from './fhir/sandbox/healthit_client';
-import {LogicaClient} from './fhir/sandbox/logica_client';
-import {AthenaClient} from './fhir/sandbox/athena_client';
-
-import {CareEvolutionClient} from './fhir/platforms/careevolution_client';
-import {CernerClient} from './fhir/platforms/cerner_client';
-import {EpicClient} from './fhir/platforms/epic_client';
-
-import {AetnaClient} from './fhir/aetna_client';
-import {BlueButtonClient} from './fhir/bluebutton_client';
-import {CignaClient} from './fhir/cigna_client';
-import {ClientConfig} from '../models/client/client-config';
-
-export function NewClient(sourceType: SourceType, source: Source, clientConfig: ClientConfig): IClient {
-
-  switch(sourceType) {
-
-    //sandbox
-    case SourceType.Athena:
-      return new AthenaClient(source, clientConfig)
-    case SourceType.HealthIT:
-      return new HealthITClient(source, clientConfig)
-    case SourceType.Logica:
-      return new LogicaClient(source, clientConfig )
-
-    //platforms
-    case SourceType.CareEvolution:
-      return new CareEvolutionClient(source, clientConfig)
-    case SourceType.Cerner:
-      return new CernerClient(source, clientConfig)
-    case SourceType.Epic:
-      return new EpicClient(source, clientConfig)
-
-    //providers
-    case SourceType.Aetna:
-      return new AetnaClient(source, clientConfig)
-
-    case SourceType.Amerigroup:
-    case SourceType.AmerigroupMedicaid:
-    case SourceType.Anthem:
-    case SourceType.AnthemBluecrossCA:
-    case SourceType.BluecrossBlueshieldKansasMedicare:
-    case SourceType.BluecrossBlueshieldKansas:
-    case SourceType.BluecrossBlueshieldNY:
-    case SourceType.BlueMedicareAdvantage:
-    case SourceType.ClearHealthAlliance:
-    case SourceType.DellChildrens:
-    case SourceType.EmpireBlue:
-    case SourceType.EmpireBlueMedicaid:
-    case SourceType.HealthyBlueLA:
-    case SourceType.HealthyBlueLAMedicaid:
-    case SourceType.HealthyBlueMO:
-    case SourceType.HealthyBlueMOMedicaid:
-    case SourceType.HealthyBlueNC:
-    case SourceType.HealthyBlueNCMedicaid:
-    case SourceType.HealthyBlueNE:
-    case SourceType.HealthyBlueSC:
-    case SourceType.HighmarkWesternNY:
-    case SourceType.SimplyHealthcareMedicaid:
-    case SourceType.SimplyHealthcareMedicare:
-    case SourceType.SummitCommunityCare:
-    case SourceType.Unicare:
-    case SourceType.UnicareMA:
-    case SourceType.UnicareMedicaid:
-      return new CareEvolutionClient(source, clientConfig)
-
-    case SourceType.UCSF:
-      return new EpicClient(source, clientConfig)
-
-    case SourceType.Cigna:
-      return new CignaClient(source, clientConfig)
-    case SourceType.BlueButton:
-      return new BlueButtonClient(source, clientConfig)
-
-    // case SourceType.Manual:
-    //   return new ManualClient(source)
-    default:
-      throw new Error(`Unknown Source Type: ${sourceType}`)
-  }
-}

frontend/src/lib/conduit/fhir/aetna_client.ts

@@ -1,25 +0,0 @@
-import {IClient} from '../interface';
-import {FHIR401Client} from './base/fhir401_r4_client';
-import {Source} from '../../models/database/source';
-import {IDatabaseRepository} from '../../database/interface';
-import {UpsertSummary} from '../../models/fasten/upsert-summary';
-import {ClientConfig} from '../../models/client/client-config';
-
-export class AetnaClient  extends FHIR401Client implements IClient {
-  constructor(source: Source, clientConfig: ClientConfig) {
-    super(source, clientConfig);
-  }
-
-  /**
-   * Aetna overrides the SyncAll function because Patient-everything operation uses a non-standard endpoint
-   * @param db
-   * @constructor
-   */
-  async SyncAll(db: IDatabaseRepository): Promise<UpsertSummary> {
-    const bundle = await this.GetResourceBundlePaginated("Patient")
-
-    const wrappedResourceModels = await this.ProcessBundle(bundle)
-    //todo, create the resources in dependency order
-    return await db.UpsertResources(wrappedResourceModels)
-  }
-}

frontend/src/lib/conduit/fhir/base/base_client.spec.ts

@@ -1,75 +0,0 @@
-import {BaseClient} from './base_client';
-import {Source} from '../../../models/database/source';
-
-// @ts-ignore
-import * as BaseClient_GetRequest from './fixtures/BaseClient_GetRequest.json';
-// @ts-ignore
-import * as BaseClient_GetFhirVersion from './fixtures/BaseClient_GetFhirVersion.json';
-import {ClientConfig} from '../../../models/client/client-config';
-
-
-class TestClient extends BaseClient {
-  constructor(source: Source) {
-    super(source, new ClientConfig());
-  }
-}
-
-describe('BaseClient', () => {
-  let client: TestClient;
-
-  beforeEach(async () => {
-    client = new TestClient(new Source({
-      "authorization_endpoint": "https://fhirsandbox.healthit.gov/open/r4/authorize",
-      "token_endpoint": "https://fhirsandbox.healthit.gov/open/r4/token",
-      "introspection_endpoint": "",
-      "issuer": "https://fhirsandbox.healthit.go",
-      "api_endpoint_base_url": "https://fhirsandbox.healthit.gov/secure/r4/fhir",
-      "client_id": "9ad3ML0upIMiawLVdM5-DiPinGcv7M",
-      "redirect_uri": "https://lighthouse.fastenhealth.com/sandbox/callback/healthit",
-      "confidential": false,
-      "source_type": "healthit",
-      "patient": "placeholder",
-      "access_token": "2e1be8c72d4d5225aae264a1fb7e1d3e",
-      "refresh_token": "",
-      "expires_at": 16649837100, //aug 11, 2497 (for testing)
-    }));
-  });
-
-  it('should be created', () => {
-    expect(client).toBeTruthy();
-  });
-
-  describe('GetRequest', () => {
-    it('should make an authorized request', async () => {
-
-      //setup
-      let response = new Response(JSON.stringify(BaseClient_GetRequest));
-      Object.defineProperty(response, "url", { value: `${client.source.api_endpoint_base_url}/Patient/${client.source.patient}`});
-      spyOn(window, "fetch").and.returnValue(Promise.resolve(response));
-
-      //test
-      const resp = await client.GetRequest(`Patient/${client.source.patient}`)
-
-      //expect
-      expect(resp.resourceType).toEqual("Patient");
-      expect(resp.id).toEqual("123d41e1-0f71-4e9f-8eb2-d1b1330201a6");
-    });
-  })
-
-  describe('GetFhirVersion', () => {
-    it('should make an authorized request', async () => {
-      //setup
-      let response = new Response(JSON.stringify(BaseClient_GetFhirVersion));
-      Object.defineProperty(response, "url", { value: `${client.source.api_endpoint_base_url}/metadata`});
-      spyOn(window, "fetch").and.returnValue(Promise.resolve(response));
-
-      //test
-      const resp = await client.GetFhirVersion()
-
-      //expect
-      expect(resp).toEqual("4.0.1");
-    });
-  });
-
-
-})

frontend/src/lib/conduit/fhir/base/base_client.ts

@@ -1,153 +0,0 @@
-import {Source} from '../../../models/database/source';
-import * as Oauth from '@panva/oauth4webapi';
-import {IResourceRaw} from '../../interface';
-import {GetEndpointAbsolutePath} from '../../../utils/endpoint_absolute_path';
-import {ClientConfig} from '../../../models/client/client-config';
-
-
-class SourceUpdateStatus {
-  is_updated: boolean = false
-  source: Source
-}
-
-// BaseClient is an abstract/partial class, its intended to be used by FHIR clients, and generically handle OAuth requests.
-export abstract class BaseClient {
-
-  private clientConfig: ClientConfig
-  private oauthClient: Oauth.Client
-  private oauthAuthorizationServer: Oauth.AuthorizationServer
-  public source: Source
-  public headers: Headers
-  public fhirVersion: string
-
-
-  protected constructor(source: Source, clientConfig: ClientConfig) {
-    this.source = source
-    this.clientConfig = clientConfig
-    this.headers = new Headers()
-
-    //init Oauth client based on source configuration
-    this.oauthClient = {
-      client_id: source.client_id,
-      client_secret: "placeholder" //this is always a placeholder, if client_secret is required (for confidential clients), token_endpoint will be Lighthouse server.
-    }
-    this.oauthAuthorizationServer = {
-      issuer: source.issuer,
-      authorization_endpoint:	source.authorization_endpoint,
-      token_endpoint:	source.token_endpoint,
-      introspection_endpoint: source.introspection_endpoint,
-    }
-  }
-
-  /**
-   * This function gets the FhirVersion as specified by the api CapabilityStatement endpoint (metadata)
-   * https://build.fhir.org/capabilitystatement.html
-   * @constructor
-   */
-  public async GetFhirVersion(): Promise<any> {
-    return this.GetRequest("metadata")
-      .then((resp) => {
-        return resp.fhirVersion
-      })
-  }
-
-  /**
-   * This function will make an authenticated request against an OAuth protected resource. If the AccessToken used has expired, it will attempt
-   * to use a refresh token (if present) to get a new AccessToken.
-   * @param resourceSubpathOrNext
-   * @constructor
-   */
-  public async GetRequest(resourceSubpathOrNext: string): Promise<any> {
-
-    //check if the url is absolute
-    let resourceUrl: string
-    if (!(resourceSubpathOrNext.indexOf('http://') === 0 || resourceSubpathOrNext.indexOf('https://') === 0)) {
-      //not absolute, so lets prefix with the source api endpoint
-      resourceUrl = `${this.source.api_endpoint_base_url.trimEnd()}/${resourceSubpathOrNext.trimStart()}`
-    } else {
-      resourceUrl = resourceSubpathOrNext
-    }
-    if(this.source.cors_relay_required){
-      //this endpoint requires a CORS relay
-      //get the path to the Fasten server, and append `cors/` and then append the request url
-      let resourceParts = new URL(resourceUrl)
-      resourceUrl = GetEndpointAbsolutePath(globalThis.location, this.clientConfig.fasten_api_endpoint_base) + `/cors/${resourceParts.hostname}${resourceParts.pathname}${resourceParts.search}`
-    }
-
-
-    //refresh the source if required
-    await this.RefreshSourceToken()
-
-    //make a request to the protected resource
-    const resp = await Oauth.protectedResourceRequest(this.source.access_token, 'GET', new URL(resourceUrl), this.headers, null)
-
-    if(resp.status >=300 || resp.status < 200){
-      // b, _ := io.ReadAll(resp.Body)
-      throw new Error(`An error occurred during request ${resourceUrl} - ${resp.status} - ${resp.statusText} ${await resp.text()}`)
-    }
-    return resp.json()
-    // err = ParseBundle(resp.Body, decodeModelPtr)
-    // return err
-  }
-
-  public async RefreshSourceToken(): Promise<boolean>{
-
-    let sourceUpdateStatus = await this.refreshExpiredTokenIfRequired(this.source)
-    this.source = sourceUpdateStatus.source
-    return sourceUpdateStatus.is_updated
-  }
-
-
-  /////////////////////////////////////////////////////////////////////////////
-  // Protected methods
-  /////////////////////////////////////////////////////////////////////////////
-
-
-  /////////////////////////////////////////////////////////////////////////////
-  // Private methods
-  /////////////////////////////////////////////////////////////////////////////
-
-  private async refreshExpiredTokenIfRequired(source: Source): Promise<SourceUpdateStatus> {
-    const sourceUpdateStatus = new SourceUpdateStatus()
-    //check if token has expired, and a refreshtoken is available
-    // Note: source.expires_at is in seconds, Date.now() is in milliseconds.
-    if(source.expires_at > Math.floor(Date.now() / 1000)) { //not expired  return
-      sourceUpdateStatus.source = source
-      return Promise.resolve(sourceUpdateStatus)
-    }
-    if(!source.refresh_token){
-      return Promise.reject(new Error("access token is expired, but no refresh token available"))
-    }
-
-    console.log("access token expired, refreshing...")
-    return Oauth.refreshTokenGrantRequest(this.oauthAuthorizationServer, this.oauthClient, source.refresh_token)
-      .then((refreshTokenResp) => {
-        return Oauth.processRefreshTokenResponse(this.oauthAuthorizationServer, this.oauthClient, refreshTokenResp)
-      })
-      .then((newToken) => {
-
-        if(newToken.access_token != source.access_token){
-          sourceUpdateStatus.is_updated = true
-          // {
-          //   access_token: 'token',
-          //   token_type: 'bearer',
-          //   expires_in: 60,
-          //   scope: 'api:read',
-          //   refresh_token: 'refresh_token',
-          // }
-
-          source.access_token = newToken.access_token as string
-          // @ts-ignore
-          source.expires_at = Math.floor(Date.now() / 1000) + parseInt(newToken.expires_in);
-
-          // update the "source" credential with new data (which will need to be sent
-          // Don't overwrite `RefreshToken` with an empty value
-          if(newToken.refresh_token != ""){
-            source.refresh_token = newToken.refresh_token as string
-          }
-        }
-        sourceUpdateStatus.source = source
-        return sourceUpdateStatus
-      })
-  }
-}

frontend/src/lib/conduit/fhir/base/fhir401_r4_client.spec.ts

@@ -1,119 +0,0 @@
-import {FHIR401Client} from './fhir401_r4_client';
-import {Source} from '../../../models/database/source';
-import {IResourceBundleRaw} from '../../interface';
-import {ResourceFhir} from '../../../models/database/resource_fhir';
-import {NewPouchdbRepositoryWebWorker} from '../../../database/pouchdb_repository';
-import {Base64} from '../../../utils/base64';
-import * as PouchDB from 'pouchdb/dist/pouchdb';
-import { v4 as uuidv4 } from 'uuid';
-
-// @ts-ignore
-import * as FHIR401Client_ProcessBundle from './fixtures/FHIR401Client_ProcessBundle.json';
-// @ts-ignore
-import * as FHIR401Client_ExtractResourceReference from './fixtures/FHIR401Client_ExtractResourceReference.json';
-import {IDatabaseRepository} from '../../../database/interface';
-import {PouchdbCrypto} from '../../../database/plugins/crypto';
-import {ClientConfig} from '../../../models/client/client-config';
-
-
-class TestClient extends FHIR401Client {
-  constructor(source: Source) {
-    super(source, new ClientConfig());
-  }
-
-  public async ProcessBundle(bundle: IResourceBundleRaw): Promise<ResourceFhir[]> {
-    return super.ProcessBundle(bundle);
-  }
-}
-
-describe('FHIR401Client', () => {
-  let client: TestClient;
-
-  beforeEach(async () => {
-    client = new TestClient(new Source({
-      "_id": "source:aetna:12345",
-      "authorization_endpoint": "https://fhirsandbox.healthit.gov/open/r4/authorize",
-      "token_endpoint": "https://fhirsandbox.healthit.gov/open/r4/token",
-      "introspection_endpoint": "",
-      "issuer": "https://fhirsandbox.healthit.go",
-      "api_endpoint_base_url": "https://fhirsandbox.healthit.gov/secure/r4/fhir",
-      "client_id": "9ad3ML0upIMiawLVdM5-DiPinGcv7M",
-      "redirect_uri": "https://lighthouse.fastenhealth.com/sandbox/callback/healthit",
-      "confidential": false,
-      "source_type": "healthit",
-      "patient": "placeholder",
-      "access_token": "2e1be8c72d4d5225aae264a1fb7e1d3e",
-      "refresh_token": "",
-      "expires_at": 16649837100, //aug 11, 2497 (for testing)
-    }));
-  });
-
-  it('should be created', () => {
-    expect(client).toBeTruthy();
-  });
-
-  describe('ProcessBundle', () => {
-    it('should correctly wrap each BundleEntry with ResourceFhir', async () => {
-
-      //setup
-
-      //test
-      const resp = await client.ProcessBundle(FHIR401Client_ProcessBundle)
-      //expect
-      expect(resp.length).toEqual(206);
-      expect(resp[0].source_resource_id).toEqual("c088b7af-fc41-43cc-ab80-4a9ab8d47cd9");
-      expect(resp[0].source_resource_type).toEqual("Patient");
-    });
-  })
-
-  describe('SyncAll', () => {
-    let repository: IDatabaseRepository;
-
-    beforeEach(async () => {
-      let current_user = uuidv4() as string
-      let cryptoConfig = await PouchdbCrypto.CryptConfig(current_user, current_user)
-      await PouchdbCrypto.StoreCryptConfig(cryptoConfig)
-      repository = NewPouchdbRepositoryWebWorker({current_user: current_user, auth_token:""}, '/database', new PouchDB("FHIR401Client-"+ current_user));
-    });
-
-    afterEach(async () => {
-      if(repository){
-        const db = await repository.GetDB()
-        db.destroy() //wipe the db.
-      }
-    })
-    it('should correctly add resources to the database', async () => {
-      //setup
-      let response = new Response(JSON.stringify(FHIR401Client_ProcessBundle));
-      Object.defineProperty(response, "url", { value: `${client.source.api_endpoint_base_url}/Patient/${client.source.patient}/$everything`});
-      spyOn(window, "fetch").and.returnValue(Promise.resolve(response));
-
-      //test
-      const resp = await client.SyncAll(repository)
-      const firstResourceFhir = resp.updatedResources[0]
-      const resourceIdParts = firstResourceFhir.split(":")
-
-      //expect
-      expect(resp.totalResources).toEqual(206);
-      expect(resp.updatedResources.length).toEqual(206);
-      expect(firstResourceFhir).toEqual('resource_fhir:b64.c291cmNlOmFldG5hOjEyMzQ1:Patient:c088b7af-fc41-43cc-ab80-4a9ab8d47cd9');
-      expect(Base64.Decode(resourceIdParts[1])).toEqual("source:aetna:12345");
-
-
-    }, 10000);
-  })
-
-  describe('ExtractResourceReference', () => {
-    it('should correctly extract resource identifier from raw resources', async () => {
-
-      //setup
-
-      //test
-      const resp = await client.ExtractResourceReference("CarePlan", FHIR401Client_ExtractResourceReference)
-      //expect
-      expect(resp.length).toEqual(2);
-      expect(resp).toEqual(['Encounter/97961321', 'Practitioner/12763770']);
-    });
-  })
-
-})

frontend/src/lib/conduit/fhir/base/fhir401_r4_client.ts

@@ -1,594 +0,0 @@
-import {IClient, IResourceBundleEntryRaw, IResourceBundleRaw, IResourceRaw} from '../../interface';
-import {BaseClient} from './base_client';
-import {Source} from '../../../models/database/source';
-import {IDatabaseRepository} from '../../../database/interface';
-import {ResourceFhir} from '../../../models/database/resource_fhir';
-import {UpsertSummary} from '../../../models/fasten/upsert-summary';
-import {ClientConfig} from '../../../models/client/client-config';
-
-export class FHIR401Client extends BaseClient implements IClient {
-
-  //clients extending this class must validate fhirVersion matches using conformance/metadata url.
-  fhirVersion = "4.0.1"
-
-  // https://build.fhir.org/ig/HL7/US-Core/
-  usCoreResources: string[] = [
-    "AllergyIntolerance",
-    //"Binary",
-    "CarePlan",
-    "CareTeam",
-    "Condition",
-    //"Coverage",
-    "Device",
-    "DiagnosticReport",
-    "DocumentReference",
-    "Encounter",
-    "Goal",
-    "Immunization",
-    //"Location",
-    //"Medication",
-    //"MedicationRequest",
-    "Observation",
-    //"Organization",
-    //"Patient",
-    //"Practitioner",
-    //"PractitionerRole",
-    "Procedure",
-    //"Provenance",
-    //"RelatedPerson",
-    // "ServiceRequest",
-    // "Specimen",
-  ]
-
-  constructor(source: Source, clientConfig: ClientConfig) {
-    super(source, clientConfig);
-  }
-
-  /**
-   * This function attempts to retrieve a Patient Bundle and sync all resources to the database
-   * @param db
-   * @constructor
-   */
-  public async SyncAll(db: IDatabaseRepository): Promise<UpsertSummary> {
-    const bundle = await this.GetPatientBundle(this.source.patient)
-
-    const wrappedResourceModels = await this.ProcessBundle(bundle)
-    //todo, create the resources in dependency order
-
-    return db.UpsertResources(wrappedResourceModels)
-
-  }
-
-  /**
-   * If Patient-everything api endpoint is unavailable (SyncAll) this function can be used to search for each resource associated with a Patient
-   * and sync them to the database.
-   * @param db
-   * @param resourceNames
-   * @constructor
-   */
-  public async SyncAllByResourceName(db: IDatabaseRepository, resourceNames: string[]): Promise<UpsertSummary>{
-    //Store the Patient
-    const patientResource = await this.GetPatient(this.source.patient)
-
-    const patientResourceFhir = new ResourceFhir()
-    patientResourceFhir.source_id = this.source._id
-    patientResourceFhir.source_resource_type = patientResource.resourceType
-    patientResourceFhir.source_resource_id = patientResource.id
-    patientResourceFhir.resource_raw = patientResource
-
-    const upsertSummary = await db.UpsertResource(patientResourceFhir)
-
-    //error map storage.
-    let syncErrors = {}
-
-    //Store all other resources.
-    for(let resourceType of resourceNames) {
-
-      try {
-        let bundle = await this.GetResourceBundlePaginated(`${resourceType}?patient=${this.source.patient}`)
-        let wrappedResourceModels = await this.ProcessBundle(bundle)
-        let resourceUpsertSummary = await db.UpsertResources(wrappedResourceModels)
-
-        upsertSummary.updatedResources = upsertSummary.updatedResources.concat(resourceUpsertSummary.updatedResources)
-        upsertSummary.totalResources += resourceUpsertSummary.totalResources
-
-
-        // check if theres any "extracted" resource references that we should sync as well
-        let extractedResourceReferences = []
-        extractedResourceReferences = wrappedResourceModels.reduce((previousVal, wrappedResource) => {
-          return previousVal.concat(this.ExtractResourceReference(wrappedResource.source_resource_type, wrappedResource.resource_raw))
-        }, extractedResourceReferences)
-
-
-        if(extractedResourceReferences.length > 0 ){
-          console.log("Extracted Resource References", extractedResourceReferences)
-
-          let extractedResourceBundle = await this.GenerateResourceBundleFromResourceIds(extractedResourceReferences)
-          let wrappedExtractedResourceBundle = await this.ProcessBundle(extractedResourceBundle)
-          let extractedResourceUpsertSummary = await db.UpsertResources(wrappedExtractedResourceBundle)
-
-          upsertSummary.updatedResources = upsertSummary.updatedResources.concat(extractedResourceUpsertSummary.updatedResources)
-          upsertSummary.totalResources += extractedResourceUpsertSummary.totalResources
-        }
-
-      }
-      catch (e) {
-        console.error(`An error occurred while processing ${resourceType} bundle ${this.source.patient}`)
-        syncErrors[resourceType] = e
-        continue
-      }
-    }
-
-    //TODO: correctly return newly inserted documents
-    return upsertSummary
-  }
-
-  /**
-   * Given a raw resource payload, this function will determine if there are references to other resources, and extract them if so
-   * This is useful because search (by patient id) is disabled for certain resource types.
-   * @param sourceResourceType
-   * @param resourceRaw
-   * @constructor
-   */
-  public ExtractResourceReference(sourceResourceType: string, resourceRaw): string[] {
-    let resourceRefs = []
-
-    switch (sourceResourceType) {
-      case "CarePlan":
-        // encounter can contain
-        //- Encounter
-        resourceRefs.push(resourceRaw.encounter?.reference)
-
-        //author can contain
-        //- Practitioner
-        //- Organization
-        //- Patient
-        //- PractitionerRole
-        //- CareTeam
-        //- RelatedPerson
-        resourceRefs.push(resourceRaw.author?.reference)
-
-
-        //contributor can contain
-        //- Practitioner
-        //- Organization
-        //- Patient
-        //- PractitionerRole
-        //- CareTeam
-        //- RelatedPerson
-        resourceRefs.push(resourceRaw.contributor?.reference)
-
-        //careTeam can contain
-        //- CareTeam
-        resourceRefs.push(resourceRaw.careTeam?.reference)
-
-        break;
-      case "CareTeam":
-        // encounter can contain
-        //- Encounter
-        resourceRefs.push(resourceRaw.encounter?.reference)
-
-        //participant[x].member can contain
-        //- Practitioner
-        //- Organization
-        //- Patient
-        //- PractitionerRole
-        //- CareTeam
-        //- RelatedPerson
-        //participant[x].onBehalfOf can contain
-        //- Organization
-        resourceRaw.participant?.map((participant) => {
-          resourceRefs.push(participant.member?.reference)
-          resourceRefs.push(participant.onBehalfOf?.reference)
-        })
-
-        //managingOrganization
-        //- Organization
-        resourceRaw.managingOrganization?.map((managingOrganization) => {
-          resourceRefs.push(managingOrganization.reference)
-        })
-        break;
-      case "Condition":
-        // recorder can contain
-        //- Practitioner
-        //- PractitionerRole
-        //- Patient
-        //- RelatedPerson
-        resourceRefs.push(resourceRaw.recorder?.reference)
-
-        // asserter can contain
-        //- Practitioner
-        //- PractitionerRole
-        //- Patient
-        //- RelatedPerson
-        resourceRefs.push(resourceRaw.asserter?.reference)
-
-        break;
-      case "DiagnosticReport":
-        //basedOn[x] can contain
-        //- CarePlan
-        //- ImmunizationRecommendation
-        //- MedicationRequest
-        //- NutritionOrder
-        //- ServiceRequest
-        resourceRaw.basedOn?.map((basedOn) => {
-          resourceRefs.push(basedOn.reference)
-        })
-
-        // performer[x] can contain
-        //- Practitioner
-        //- PractitionerRole
-        //- Organization
-        //- CareTeam
-        resourceRaw.performer?.map((performer) => {
-          resourceRefs.push(performer.reference)
-        })
-        break;
-      case "DocumentReference":
-        //author[x] can contain
-        //- Practitioner
-        //- Organization
-        //- Patient
-        //- PractitionerRole
-        //- CareTeam
-        //- Device
-        resourceRaw.author?.map((author) => {
-          resourceRefs.push(author.reference)
-        })
-
-        //authenticator can contain
-        //- Practitioner
-        //- Organization
-        //- PractitionerRole
-        resourceRefs.push(resourceRaw.authenticator?.reference)
-
-        // custodian can contain
-        //- Organization
-        resourceRefs.push(resourceRaw.custodian?.reference)
-
-        // relatesTo.target
-        //- DocumentReference
-        resourceRaw.relatesTo?.map((relatesTo) => {
-          resourceRefs.push(relatesTo.target?.reference)
-        })
-
-        //content.attachment can contain
-        //- Attachment
-        break
-      case "Encounter":
-        // basedOn[x] can contain
-        //- ServiceRequest
-        resourceRaw.basedOn?.map((basedOn) => {
-          resourceRefs.push(basedOn.reference)
-        })
-
-        //participant[x].individual can contain
-        //- Practitioner
-        //- PractitionerRole
-        //- RelatedPerson
-        resourceRaw.participant?.map((participant) => {
-          resourceRefs.push(participant.individual?.reference)
-        })
-
-        //reasonReference[x] can contain
-        //- Condition
-        //- Procedure
-        //- Observation
-        //- ImmunizationRecommendation
-        resourceRaw.reasonReference?.map((reasonReference) => {
-          resourceRefs.push(reasonReference.reference)
-        })
-
-        //hospitalization.origin can contain
-        //- Location
-        //- Organization
-        resourceRefs.push(resourceRaw.hospitalization?.origin?.reference)
-
-        //hospitalization.destination can contain
-        //- Location
-        //- Organization
-        resourceRefs.push(resourceRaw.hospitalization?.destination?.reference)
-
-        //location[x].location can contain
-        //- Location
-        resourceRaw.location?.map((location) => {
-          resourceRefs.push(location.location?.reference)
-        })
-
-        //serviceProvider can contain
-        //- Organization
-        resourceRefs.push(resourceRaw.serviceProvider?.reference)
-
-        break
-      case "Immunization":
-        // location can contain
-        //- Location
-        resourceRefs.push(resourceRaw.location?.reference)
-
-        // manufacturer can contain
-        //- Organization
-        resourceRefs.push(resourceRaw.manufacturer?.reference)
-
-        //performer[x].actor can contain
-        //- Practitioner | PractitionerRole | Organization
-        resourceRaw.performer?.map((performer) => {
-          resourceRefs.push(performer.actor?.reference)
-        })
-
-        //reasonReference[x] can contain
-        //- Condition | Observation | DiagnosticReport
-        resourceRaw.reasonReference?.map((reasonReference) => {
-          resourceRefs.push(reasonReference.reference)
-        })
-
-        //protocolApplied[x].authority can contain
-        //- Organization
-        resourceRaw.protocolApplied?.map((protocolApplied) => {
-          resourceRefs.push(protocolApplied.authority?.reference)
-        })
-        break
-      case "Location":
-        // managingOrganization can contain
-        //- Organization
-        resourceRefs.push(resourceRaw.managingOrganization?.reference)
-
-        // partOf can contain
-        //- Location
-        resourceRefs.push(resourceRaw.partOf?.reference)
-
-        break
-      case "MedicationRequest":
-        // reported.reportedReference can contain
-        //- Practitioner
-        //- Organization
-        //- Patient
-        //- PractitionerRole
-        //- RelatedPerson
-        resourceRefs.push(resourceRaw.reported?.reportedReference?.reference)
-
-        // medication[x] can contain
-        //- Medication
-        resourceRefs.push(resourceRaw.reported?.reportedReference?.reference)
-
-        // requester can contain
-        //- Practitioner
-        //- Organization
-        //- Patient
-        //- PractitionerRole
-        //- RelatedPerson
-        //- Device
-        resourceRefs.push(resourceRaw.requester?.reference)
-
-        // performer can contain
-        //- Practitioner | PractitionerRole | Organization | Patient | Device | RelatedPerson | CareTeam
-        resourceRefs.push(resourceRaw.performer?.reference)
-        // recorder can contain
-        //- Practitioner | PractitionerRole
-        resourceRefs.push(resourceRaw.recorder?.reference)
-
-        //TODO: reasonReference
-        //TODO: basedOn
-        //TODO: insurance
-
-        // dispenseRequest.performer can contain
-        //- Organization
-        resourceRefs.push(resourceRaw.dispenseRequest?.performer?.reference)
-        break
-      case "Observation":
-        //basedOn[x] can contain
-        //- CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest
-        resourceRaw.basedOn?.map((basedOn) => {
-          resourceRefs.push(basedOn.reference)
-        })
-
-        // partOf[x] can contain
-        //- MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy
-        resourceRaw.partOf?.map((partOf) => {
-          resourceRefs.push(partOf.reference)
-        })
-        // performer[x] can contain
-        //- Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson
-        resourceRaw.performer?.map((performer) => {
-          resourceRefs.push(performer.reference)
-        })
-        // device can contain
-        //- Device | DeviceMetric
-        resourceRefs.push(resourceRaw.device?.reference)
-
-        break
-      case "PractitionerRole":
-        // practitioner can contain
-        //- Practitioner
-        resourceRefs.push(resourceRaw.practitioner?.reference)
-
-        //organization can contain
-        //- Organization
-        resourceRefs.push(resourceRaw.organization?.reference)
-
-        //location can contain
-        //- Location
-        resourceRefs.push(resourceRaw.location?.reference)
-
-        //TODO: healthcareService
-        //TODO: endpoint
-        break
-      case "ServiceRequest":
-        // basedOn[x] can contain
-        //- CarePlan | ServiceRequest | MedicationRequest
-        resourceRaw.basedOn?.map((basedOn) => {
-          resourceRefs.push(basedOn.reference)
-        })
-
-        //requester can contain
-        //- Practitioner
-        //- Organization
-        //- Patient
-        //- PractitionerRole
-        //- RelatedPerson
-        //- Device
-        resourceRefs.push(resourceRaw.requester?.reference)
-
-        //performer[x] can contain
-        //- Practitioner | PractitionerRole | Organization | CareTeam | HealthcareService | Patient | Device | RelatedPerson
-        resourceRaw.performer?.map((performer) => {
-          resourceRefs.push(performer.reference)
-        })
-
-        //locationReference[x] an contain
-        //-Location
-        resourceRaw.locationReference?.map((locationReference) => {
-          resourceRefs.push(locationReference.reference)
-        })
-
-        //reasonReference[x] can contain
-        //-Condition
-        //-Observation
-        //-DiagnosticReport
-        //-DocumentReference
-        resourceRaw.reasonReference?.map((reasonReference) => {
-          resourceRefs.push(reasonReference.reference)
-        })
-
-        //insurance[x] can contain
-        //- Coverage | ClaimResponse
-        resourceRaw.insurance?.map((insurance) => {
-          resourceRefs.push(insurance.reference)
-        })
-        break
-    }
-
-    // remove all null values, remove all duplicates
-    let cleanResourceRefs = resourceRefs.filter(i => !(typeof i === 'undefined' || i === null));
-    cleanResourceRefs = [...new Set(cleanResourceRefs)]
-    return cleanResourceRefs
-  }
-
-  /**
-   * This function is used to sync all resources from a Bundle file. Not applicable to this Client
-   * @param db
-   * @param bundleFile
-   * @constructor
-   */
-  public async SyncAllFromBundleFile(db: IDatabaseRepository, bundleFile: any): Promise<UpsertSummary> {
-    return Promise.reject(new Error("not implemented"));
-  }
-
-  /////////////////////////////////////////////////////////////////////////////
-  // Protected methods
-  /////////////////////////////////////////////////////////////////////////////
-  /**
-   * This function attempts to retrieve the Patient Bundle using the Patient-everything api endpoint (if available)
-   * This response may be paginated
-   * https://hl7.org/fhir/operation-patient-everything.html
-   * @param patientId
-   * @constructor
-   * @protected
-   */
-  protected GetPatientBundle(patientId: string): Promise<any> {
-    return this.GetResourceBundlePaginated(`Patient/${patientId}/$everything`)
-  }
-
-  /**
-   * This function retrieves a patient resource
-   * @param patientId
-   * @constructor
-   * @protected
-   */
-  protected GetPatient(patientId: string): Promise<IResourceRaw> {
-    return this.GetRequest(`Patient/${patientId}`)
-  }
-
-  /**
-   * This function parses a FHIR Bundle and wraps each BundleEntry resource in a ResourceFhir object which can be stored in the DB.
-   * @param bundle
-   * @constructor
-   * @protected
-   */
-  protected async ProcessBundle(bundle: IResourceBundleRaw): Promise<ResourceFhir[]> {
-    // console.log(bundle)
-    // process each entry in bundle
-    return bundle.entry
-      .filter((bundleEntry) => {
-        return bundleEntry.resource.id // keep this entry if it has an ID, skip otherwise.
-      })
-      .map((bundleEntry) => {
-        const wrappedResourceModel = new ResourceFhir()
-        wrappedResourceModel.fhir_version = this.fhirVersion
-        wrappedResourceModel.source_id = this.source._id
-        wrappedResourceModel.source_resource_id = bundleEntry.resource.id
-        wrappedResourceModel.source_resource_type = bundleEntry.resource.resourceType
-        wrappedResourceModel.resource_raw = bundleEntry.resource
-        // TODO find a way to safely/consistently get the resource updated date (and other metadata) which shoudl be added to the model.
-        // wrappedResourceModel.updated_at = bundleEntry.resource.meta?.lastUpdated
-        return wrappedResourceModel
-      })
-  }
-
-  /**
-   * Given a list of resource ids (Patient/xxx, Observation/yyyy), request these resources and generate a pseudo-bundle file
-   * @param resourceIds
-   * @constructor
-   * @protected
-   */
-  protected async GenerateResourceBundleFromResourceIds(resourceIds: string[]): Promise<IResourceBundleRaw>{
-
-    resourceIds = [...new Set(resourceIds)] //make sure they are unique references.
-    let rawResourceRefs = await Promise.all(resourceIds.map(async (extractedResourceRef) => {
-      return {
-        resource: await this.GetRequest(extractedResourceRef) as IResourceRaw
-      } as IResourceBundleEntryRaw
-    }))
-
-    return {resourceType: "Bundle", entry: rawResourceRefs}
-  }
-
-  /**
-   * Retrieve a resource bundle. While "next" link is present in response, continue to request urls and append BundleEntries
-   * @param relativeResourcePath
-   * @constructor
-   * @private
-   */
-  protected async GetResourceBundlePaginated(relativeResourcePath: string): Promise<IResourceBundleRaw> {
-    // https://www.hl7.org/fhir/patient-operation-everything.html
-
-    const bundle = await this.GetRequest(relativeResourcePath) as IResourceBundleRaw
-
-    let next: string
-    let prev: string
-    let self: string
-    for(let link of bundle.link || []){
-      if(link.relation == "next"){
-        next = link.url
-      } else if(link.relation == "self"){
-        self = link.url
-      } else if(link.relation == "previous"){
-        prev = link.url
-      }
-    }
-
-    while(next && next != self && next != prev){
-      console.debug(`Paginated request => ${next}`)
-      let nextBundle = await this.GetRequest(next) as IResourceBundleRaw
-      bundle.entry = bundle.entry.concat(nextBundle.entry)
-
-      next = "" //reset the pointers
-      self = ""
-      prev = ""
-      for(let link of nextBundle.link){
-        if(link.relation == "next"){
-          next = link.url
-        } else if(link.relation == "self"){
-          self = link.url
-        } else if(link.relation == "previous"){
-          prev = link.url
-        }
-      }
-    }
-
-    return bundle
-  }
-
-  /////////////////////////////////////////////////////////////////////////////
-  // Private methods
-  /////////////////////////////////////////////////////////////////////////////
-}

frontend/src/lib/conduit/fhir/base/fixtures/BaseClient_GetRequest.json

@@ -1,159 +0,0 @@
-{
-  "resourceType": "Patient",
-  "id": "123d41e1-0f71-4e9f-8eb2-d1b1330201a6",
-  "meta": {
-    "versionId": "1.0"
-  },
-  "extension": [
-    {
-      "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
-      "extension": [
-        {
-          "url": "ombCategory",
-          "valueCoding": {
-            "system": "urn:oid:2.16.840.1.113883.6.238",
-            "code": "2054-5",
-            "display": "Black or African American"
-          }
-        },
-        {
-          "url": "text",
-          "valueString": "Black or African American"
-        }
-      ]
-    },
-    {
-      "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
-      "extension": [
-        {
-          "url": "ombCategory",
-          "valueCoding": {
-            "system": "urn:oid:2.16.840.1.113883.6.238",
-            "code": "2135-2",
-            "display": "Hispanic or Latino"
-          }
-        },
-        {
-          "url": "text",
-          "valueString": "Hispanic or Latino"
-        }
-      ]
-    },
-    {
-      "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName",
-      "valueString": "Ramona980 Franco581"
-    },
-    {
-      "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex",
-      "valueCode": "M"
-    },
-    {
-      "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
-      "valueCode": "masked"
-    }
-  ],
-  "identifier": [
-    {
-      "system": "https://github.com/synthetichealth/synthea",
-      "value": "123d41e1-0f71-4e9f-8eb2-d1b1330201a6"
-    },
-    {
-      "type": {
-        "coding": [
-          {
-            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
-            "code": "MR",
-            "display": "Medical Record Number"
-          }
-        ]
-      },
-      "system": "http://hospital.smarthealthit.org",
-      "value": "123d41e1-0f71-4e9f-8eb2-d1b1330201a6"
-    },
-    {
-      "type": {
-        "coding": [
-          {
-            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
-            "code": "SS",
-            "display": "Social Security Number"
-          }
-        ]
-      },
-      "system": "http://hl7.org/fhir/sid/us-ssn",
-      "value": "999-50-6731"
-    },
-    {
-      "type": {
-        "coding": [
-          {
-            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
-            "code": "DL",
-            "display": "Drivers License"
-          }
-        ]
-      },
-      "system": "urn:oid:2.16.840.1.113883.4.3.25",
-      "value": "S99957478"
-    }
-  ],
-  "name": [
-    {
-      "use": "official",
-      "family": "Gutiérrez115",
-      "given": [
-        "Hugo693"
-      ],
-      "prefix": [
-        "Mr."
-      ]
-    }
-  ],
-  "telecom": [
-    {
-      "system": "phone",
-      "value": "555-914-6475",
-      "use": "home"
-    }
-  ],
-  "gender": "male",
-  "birthDate": "1969-01-12",
-  "address": [
-    {
-      "line": [
-        "[\"293 Douglas Ramp\"]"
-      ],
-      "city": "Natick",
-      "state": "MA",
-      "postalCode": "01999",
-      "country": "US",
-      "period": {
-        "start": "1969-01-12T00:00:00+00:00"
-      }
-    }
-  ],
-  "maritalStatus": {
-    "coding": [
-      {
-        "system": "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus",
-        "code": "M",
-        "display": "M"
-      }
-    ],
-    "text": "M"
-  },
-  "multipleBirthBoolean": false,
-  "communication": [
-    {
-      "language": {
-        "coding": [
-          {
-            "system": "urn:ietf:bcp:47",
-            "code": "es",
-            "display": "Spanish"
-          }
-        ]
-      }
-    }
-  ]
-}

frontend/src/lib/conduit/fhir/base/fixtures/FHIR401Client_ExtractResourceReference.json

@@ -1,41 +0,0 @@
-{
-  "resourceType": "CarePlan",
-  "id": "197543976",
-  "meta": {
-    "versionId": "1",
-    "lastUpdated": "2021-10-04T14:46:33.000Z"
-  },
-  "text": {
-    "status": "additional",
-    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Care Plan</b></p><p><b>Patient</b>: SMART, NANCYU NHA EEEEEE</p><p><b>Title</b>: Comorbidities found via Retrieve Dx</p><p><b>Description</b>: Malnutrition:Severe --- Inputs [Height: 165.1, Weight: 25, BMI (Calculated): 9.171615976368047]\n\nAnoxic Brain Injury\n\n</p><p><b>Status</b>: Active</p><p><b>Intent</b>: Plan</p><p><b>Category</b>: Assessment and Plan of Treatment</p><p><b>Author</b>: P., MD, Cardio</p><p><b>Effective Period</b>: Oct  4, 2021  2:46 P.M. UTC</p></div>"
-  },
-  "status": "active",
-  "intent": "plan",
-  "category": [
-    {
-      "coding": [
-        {
-          "system": "http://hl7.org/fhir/us/core/CodeSystem/careplan-category",
-          "code": "assess-plan",
-          "display": "Assessment and Plan of Treatment"
-        }
-      ],
-      "text": "Assessment and Plan of Treatment"
-    }
-  ],
-  "title": "Comorbidities found via Retrieve Dx",
-  "subject": {
-    "reference": "Patient/12724066",
-    "display": "SMART, NANCYU NHA EEEEEE"
-  },
-  "encounter": {
-    "reference": "Encounter/97961321"
-  },
-  "period": {
-    "start": "2021-10-04T14:46:33.000Z"
-  },
-  "author": {
-    "reference": "Practitioner/12763770",
-    "display": "P., MD, Cardio"
-  }
-}

frontend/src/lib/conduit/fhir/bluebutton_client.ts

@@ -1,26 +0,0 @@
-import {IClient} from '../interface';
-import {FHIR401Client} from './base/fhir401_r4_client';
-import {Source} from '../../models/database/source';
-import {IDatabaseRepository} from '../../database/interface';
-import {UpsertSummary} from '../../models/fasten/upsert-summary';
-import {ClientConfig} from '../../models/client/client-config';
-
-export class BlueButtonClient  extends FHIR401Client implements IClient {
-  constructor(source: Source, clientConfig: ClientConfig) {
-    super(source, clientConfig);
-  }
-
-  /**
-   * BlueButton overrides the SyncAll function because Patient-everything operation is not available.
-   * @param db
-   * @constructor
-   */
-  async SyncAll(db: IDatabaseRepository): Promise<UpsertSummary> {
-    const supportedResources: string[] = [
-      "ExplanationOfBenefit",
-      "Coverage",
-    ]
-
-    return this.SyncAllByResourceName(db, supportedResources)
-  }
-}

frontend/src/lib/conduit/fhir/cigna_client.ts

@@ -1,11 +0,0 @@
-import {IClient} from '../interface';
-import {FHIR401Client} from './base/fhir401_r4_client';
-import {Source} from '../../models/database/source';
-import {ClientConfig} from '../../models/client/client-config';
-
-export class CignaClient  extends FHIR401Client implements IClient {
-  constructor(source: Source, clientConfig: ClientConfig) {
-    super(source, clientConfig);
-  }
-
-}

frontend/src/lib/conduit/fhir/platforms/careevolution_client.ts

@@ -1,13 +0,0 @@
-import {IClient} from '../../interface';
-import {FHIR401Client} from '../base/fhir401_r4_client';
-import {Source} from '../../../models/database/source';
-import {ClientConfig} from '../../../models/client/client-config';
-
-export class CareEvolutionClient  extends FHIR401Client implements IClient {
-  constructor(source: Source, clientConfig: ClientConfig) {
-    super(source, clientConfig);
-    //CareEvolution API requires the following Accept header for every request
-    this.headers.set("Accept","application/json+fhir")
-  }
-
-}

frontend/src/lib/conduit/fhir/platforms/cerner_client.ts

@@ -1,41 +0,0 @@
-import {IClient} from '../../interface';
-import {FHIR401Client} from '../base/fhir401_r4_client';
-import {Source} from '../../../models/database/source';
-import {IDatabaseRepository} from '../../../database/interface';
-import {UpsertSummary} from '../../../models/fasten/upsert-summary';
-import {ClientConfig} from '../../../models/client/client-config';
-
-export class CernerClient  extends FHIR401Client implements IClient {
-  constructor(source: Source, clientConfig: ClientConfig) {
-    super(source, clientConfig);
-    //Cerner API requires the following Accept header for every request
-    this.headers.set("Accept","application/json+fhir")
-  }
-
-  /**
-   * Cerner overrides the SyncAll function because Patient-everything operation is not available.
-   * @param db
-   * @constructor
-   */
-  async SyncAll(db: IDatabaseRepository): Promise<UpsertSummary> {
-    const supportedResources: string[] = this.usCoreResources.concat([
-      "Account",
-      "Appointment",
-      "Consent",
-      "FamilyMemberHistory",
-      "InsurancePlan",
-      "MedicationRequest",
-      "NutritionOrder",
-      "Person",
-      "Provenance",
-      "Questionnaire",
-      "QuestionnaireResponse",
-      "RelatedPerson",
-      "Schedule",
-      "ServiceRequest",
-      "Slot",
-    ])
-
-    return this.SyncAllByResourceName(db, supportedResources)
-  }
-}

frontend/src/lib/conduit/fhir/platforms/epic_client.ts

@@ -1,39 +0,0 @@
-import {IClient} from '../../interface';
-import {FHIR401Client} from '../base/fhir401_r4_client';
-import {Source} from '../../../models/database/source';
-import {IDatabaseRepository} from '../../../database/interface';
-import {UpsertSummary} from '../../../models/fasten/upsert-summary';
-import {ClientConfig} from '../../../models/client/client-config';
-
-export class EpicClient  extends FHIR401Client implements IClient {
-  constructor(source: Source, clientConfig: ClientConfig) {
-    super(source, clientConfig);
-    //Epic API requires the following Accept header for every request
-    this.headers.set("Accept","application/json+fhir")
-  }
-
-  /**
-   * Epic overrides the SyncAll function because Patient-everything operation is not available.
-   * @param db
-   * @constructor
-   */
-  async SyncAll(db: IDatabaseRepository): Promise<UpsertSummary> {
-    const supportedResources: string[] = this.usCoreResources.concat([
-      "Consent",
-      "FamilyMemberHistory",
-      "InsurancePlan",
-      "MedicationRequest",
-      "NutritionOrder",
-      "Person",
-      "Provenance",
-      "Questionnaire",
-      "QuestionnaireResponse",
-      "RelatedPerson",
-      "Schedule",
-      "ServiceRequest",
-      "Slot",
-    ])
-
-    return this.SyncAllByResourceName(db, supportedResources)
-  }
-}

frontend/src/lib/conduit/fhir/sandbox/athena_client.ts

@@ -1,23 +0,0 @@
-import {IClient} from '../../interface';
-import {FHIR401Client} from '../base/fhir401_r4_client';
-import {Source} from '../../../models/database/source';
-import {IDatabaseRepository} from '../../../database/interface';
-import {UpsertSummary} from '../../../models/fasten/upsert-summary';
-import {ClientConfig} from '../../../models/client/client-config';
-
-export class AthenaClient  extends FHIR401Client implements IClient {
-  constructor(source: Source, clientConfig: ClientConfig) {
-    super(source, clientConfig);
-  }
-
-  /**
-   * Athena overrides the SyncAll function because Patient-everything operation is not available.
-   * @param db
-   * @constructor
-   */
-  async SyncAll(db: IDatabaseRepository): Promise<UpsertSummary> {
-    const supportedResources: string[] = this.usCoreResources
-
-    return this.SyncAllByResourceName(db, supportedResources)
-  }
-}

frontend/src/lib/conduit/fhir/sandbox/healthit_client.ts

@@ -1,39 +0,0 @@
-import {IClient} from '../../interface';
-import {FHIR401Client} from '../base/fhir401_r4_client';
-import {Source} from '../../../models/database/source';
-import {IDatabaseRepository} from '../../../database/interface';
-import {UpsertSummary} from '../../../models/fasten/upsert-summary';
-import {ClientConfig} from '../../../models/client/client-config';
-
-export class HealthITClient  extends FHIR401Client implements IClient {
-  constructor(source: Source, clientConfig: ClientConfig) {
-    super(source, clientConfig);
-    //HealthIT API requires the following Accept header for every request
-    this.headers.set("Accept","application/json+fhir")
-  }
-
-  /**
-   * HealthIT overrides the SyncAll function because Patient-everything operation is not available.
-   * @param db
-   * @constructor
-   */
-  async SyncAll(db: IDatabaseRepository): Promise<UpsertSummary> {
-    const supportedResources: string[] = this.usCoreResources.concat([
-      "Consent",
-      "FamilyMemberHistory",
-      "InsurancePlan",
-      "MedicationRequest",
-      "NutritionOrder",
-      "Person",
-      "Provenance",
-      "Questionnaire",
-      "QuestionnaireResponse",
-      "RelatedPerson",
-      "Schedule",
-      "ServiceRequest",
-      "Slot",
-    ])
-
-    return this.SyncAllByResourceName(db, supportedResources)
-  }
-}

frontend/src/lib/conduit/fhir/sandbox/logica_client.ts

@@ -1,11 +0,0 @@
-import {IClient} from '../../interface';
-import {FHIR401Client} from '../base/fhir401_r4_client';
-import {Source} from '../../../models/database/source';
-import {IDatabaseRepository} from '../../../database/interface';
-import {ClientConfig} from '../../../models/client/client-config';
-
-export class LogicaClient  extends FHIR401Client implements IClient {
-  constructor(source: Source, clientConfig: ClientConfig) {
-    super(source, clientConfig);
-  }
-}

frontend/src/lib/conduit/interface.ts

@@ -1,58 +0,0 @@
-import {IDatabaseRepository} from '../database/interface';
-import {UpsertSummary} from '../models/fasten/upsert-summary';
-import {Source} from '../models/database/source';
-
-export interface IClient {
-  fhirVersion: string
-  source: Source
-  GetRequest(resourceSubpath: string): Promise<any>
-  GetFhirVersion(): Promise<any>
-  RefreshSourceToken(): Promise<boolean>
-
-  /**
-   * This function attempts to retrieve a Patient Bundle and sync all resources to the database
-   * @param db
-   * @constructor
-   */
-  SyncAll(db: IDatabaseRepository): Promise<UpsertSummary>
-
-
-  SyncAllByResourceName(db: IDatabaseRepository, resourceNames: string[]): Promise<UpsertSummary>
-
-  //Manual client ONLY functions
-  SyncAllFromBundleFile(db: IDatabaseRepository, bundleFile: any): Promise<UpsertSummary>
-}
-
-//This is the "raw" Fhir resource
-export interface IResourceRaw {
-  resourceType: string
-  id?: string
-  meta?: IResourceMetaRaw
-}
-// This is the "raw" Fhir Bundle resource
-export interface IResourceBundleRaw {
-  resourceType: string
-  id?: string
-  entry: IResourceBundleEntryRaw[]
-  total?: number
-  link?: IResourceBundleLinkRaw[]
-  meta?: IResourceMetaRaw
-}
-
-export interface IResourceBundleLinkRaw {
-  id?: string
-  relation: string
-  url: string
-}
-
-export interface IResourceBundleEntryRaw {
-  id?: string
-  fullUrl?: string
-  resource: IResourceRaw
-}
-
-export interface IResourceMetaRaw {
-  id?: string
-  versionId?: string
-  lastUpdated: string
-}

frontend/src/lib/database/constants.ts

@@ -1,4 +0,0 @@
-export enum DocType {
-  Source = "source",
-  ResourceFhir = "resource_fhir"
-}

frontend/src/lib/database/interface.ts

@@ -1,49 +0,0 @@
-import {Source} from '../models/database/source';
-import {ResourceFhir} from '../models/database/resource_fhir';
-import {SourceSummary} from '../models/fasten/source-summary';
-import {Summary} from '../models/fasten/summary';
-import {User} from '../models/fasten/user';
-import {UpsertSummary} from '../models/fasten/upsert-summary';
-// import {SourceSummary} from '../../app/models/fasten/source-summary';
-
-export interface IDatabaseDocument {
-  _id?: string
-  _rev?: string
-  doc_type: string
-  updated_at?: string
-
-  populateId(): void
-  base64Id(): string
-}
-
-export interface IDatabasePaginatedResponse {
-  offset: number,
-  total_rows: number,
-  rows: any[]
-}
-export interface IDatabaseRepository {
-  GetDB(skipEncryption?: boolean): any
-  Close(): void
-
-  // CreateUser(*models.User) error
-  // GetUserByEmail(context.Context, string) (*models.User, error)
-  // GetCurrentUser(context.Context) *models.User
-
-  UpsertSource(source: Source): Promise<UpsertSummary>
-  GetSource(source_id: string): Promise<Source>
-  DeleteSource(source_id: string): Promise<boolean>
-  GetSourceSummary(source_id: string): Promise<SourceSummary>
-  GetSources(): Promise<IDatabasePaginatedResponse>
-  IsDatabasePopulated(): Promise<boolean>
-
-  // UpsertResource(context.Context, *models.ResourceFhir) error
-  // GetResourceBySourceType(context.Context, string, string) (*models.ResourceFhir, error)
-  // GetResourceBySourceId(context.Context, string, string) (*models.ResourceFhir, error)
-  // ListResources(context.Context, models.ListResourceQueryOptions) ([]models.ResourceFhir, error)
-  // GetPatientForSources(ctx context.Context) ([]models.ResourceFhir, error)
-  UpsertResource(resource: ResourceFhir): Promise<UpsertSummary>
-  UpsertResources(resources: ResourceFhir[]): Promise<UpsertSummary>
-  GetResource(resource_id: string): Promise<ResourceFhir>
-  GetResources(): Promise<IDatabasePaginatedResponse>
-  GetResourcesForSource(source_id: string, source_resource_type?: string): Promise<IDatabasePaginatedResponse>
-}

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

@@ -1,159 +0,0 @@
-// This is a Typescript module that recreates the functionality defined in https://github.com/calvinmetcalf/crypto-pouch/blob/master/index.js
-// This file only exists because the PouchDB crypto plugin must work in both the browser and web-worker environment (where `window` is
-// undefined and causes errors).
-// Also, crypto-pouch does not support storing encrypted data in the remote database by default, which I'm attempting to do by commenting out the
-// NO_COUCH error.
-//
-// We've attempted to use the Typescript Module Plugin/Augmentation pattern to modify the global `pouchdb` object, however that
-// failed for a variety of reasons, so instead we're using a PouchdbCrypto class with static methods to re-implement the crypto logic
-//
-//
-// See:
-// - https://github.com/calvinmetcalf/crypto-pouch/blob/master/index.js
-// - https://www.typescriptlang.org/docs/handbook/declaration-files/templates/module-plugin-d-ts.html
-// - https://www.typescriptlang.org/docs/handbook/declaration-merging.html
-// - https://www.typescriptlang.org/docs/handbook/declaration-files/templates/global-plugin-d-ts.html
-// - https://www.typescriptlang.org/docs/handbook/declaration-files/templates/global-modifying-module-d-ts.html
-// - https://stackoverflow.com/questions/35074713/extending-typescript-global-object-in-node-js
-// - https://github.com/Microsoft/TypeScript/issues/15818
-
-import * as Crypt from 'garbados-crypt';
-import { openDB, deleteDB, wrap, unwrap } from 'idb';
-
-// const Crypt = require()
-
-const LOCAL_ID = '_local/crypto'
-const IGNORE = ['_id', '_rev', '_deleted', '_conflicts']
-
-// const NO_COUCH = 'crypto-pouch does not work with pouchdb\'s http adapter. Use a local adapter instead.'
-
-export class PouchdbCryptoOptions {
-  ignore?: string[]
-}
-
-export class PouchdbCryptConfig {
-  username: string
-  key: string
-  config: string
-}
-
-
-export class PouchdbCrypto {
-  private static async localIdb(){
-    const dbPromise = openDB('crypto-store', 1, {
-      upgrade(db) {
-        db.createObjectStore('crypto');
-      },
-    });
-
-    return await dbPromise
-  }
-
-
-  public static async CryptConfig(key: string, username): Promise<PouchdbCryptConfig>{
-    const _crypt = new Crypt(key)
-    let exportString = await _crypt.export()
-    return {username: username, key: key, config: exportString}
-  }
-
-  public static async StoreCryptConfig(cryptConfig: PouchdbCryptConfig) {
-    const localDb = await PouchdbCrypto.localIdb()
-    await localDb.put('crypto', JSON.stringify(cryptConfig), `encryption_data_${cryptConfig.username}`)
-  }
-
-  public static async RetrieveCryptConfig(currentUser: string): Promise<PouchdbCryptConfig>{
-    const localDb = await PouchdbCrypto.localIdb()
-    let cryptConfigStr = await localDb.get('crypto',`encryption_data_${currentUser}`)
-    if(!cryptConfigStr){
-      throw new Error("crypto configuration not set")
-    }
-    return JSON.parse(cryptConfigStr) as PouchdbCryptConfig
-  }
-  public static async DeleteCryptConfig(currentUser: string): Promise<void>{
-    const localDb = await PouchdbCrypto.localIdb()
-    return await localDb.delete('crypto',`encryption_data_${currentUser}`)
-  }
-
-
-  public static async crypto(db, cryptConfig: PouchdbCryptConfig, options: PouchdbCryptoOptions = {}) {
-    // if (db.adapter === 'http') {
-    //   throw new Error(NO_COUCH)
-    // }
-    // if (typeof password === 'object') {
-    //   // handle `db.crypto({ password, ...options })`
-    //   options = password
-    //   password = password.password
-    //   delete options.password
-    // }
-    // setup ignore list
-    db._ignore = IGNORE.concat(options.ignore || [])
-
-    if(!cryptConfig || !cryptConfig.key || !cryptConfig.config){
-      throw new Error("crypto configuration file is required")
-    }
-
-    // setup crypto helper
-    const trySetup = async () => {
-      // try saving credentials to a local doc
-      try {
-        // // first we try to get saved creds from the local doc
-        // const localDb = await PouchdbCrypto.localIdb()
-        // let exportString = await localDb.get('crypto',`encryption_data_${db.name}`)
-        // if(!exportString){
-        //   // no existing encryption key found
-        //
-        //   // do first-time setup
-        //   db._crypt = new Crypt(password)
-        //   let exportString = await db._crypt.export()
-        //   await localDb.put('crypto', exportString, `encryption_data_${db.name}`)
-        // } else {
-        //
-        // }
-
-        db._crypt = await Crypt.import(cryptConfig.key, cryptConfig.config)
-
-      } catch (err) {
-        throw err
-      }
-    }
-    await trySetup()
-    // instrument document transforms
-    db.transform({
-      incoming: async (doc) => {
-        // if no crypt, ex: after .removeCrypto(), just return the doc
-        if (!db._crypt) {
-          return doc
-        }
-        if (doc._attachments && !db._ignore.includes('_attachments')) {
-          throw new Error('Attachments cannot be encrypted. Use {ignore: "_attachments"} option')
-        }
-        let encrypted: any = {}
-        for (let key of db._ignore) {
-          // attach ignored fields to encrypted doc
-          if (key in doc) encrypted[key] = doc[key]
-        }
-        encrypted.payload = await db._crypt.encrypt(JSON.stringify(doc))
-        return encrypted
-      },
-      outgoing: async (doc) => {
-        return await this.decryptDocument(db, doc)
-      }
-    })
-    return db
-  }
-  public static async decryptDocument(db, doc):Promise<any>{
-    // if no crypt, ex: after .removeCrypto(), just return the doc
-    if (!db._crypt) { return doc }
-    let decryptedString = await db._crypt.decrypt(doc.payload)
-    let decrypted = JSON.parse(decryptedString)
-    for (let key of db._ignore) {
-      // patch decrypted doc with ignored fields
-      if (key in doc) decrypted[key] = doc[key]
-    }
-    return decrypted
-  }
-
-  public static removeCrypto(db) {
-    delete db._crypt
-  }
-}

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

@@ -1,101 +0,0 @@
-// This is a Typescript module that recreates the functionality defined in https://github.com/pouchdb/upsert/blob/master/index.js
-// This file only exists because the PouchDB upsert plugin must work in both the browser and web-worker environment (where `window` is
-// undefined and causes errors).
-//
-// We've attempted to use the Typescript Module Plugin/Augmentation pattern to modify the global `pouchdb` object, however that
-// failed for a variety of reasons, so instead we're using a PouchdbUpsert class with static methods to re-implement the upsert logic
-//
-// See:
-// - https://github.com/pouchdb/upsert/blob/master/index.js
-// - https://www.typescriptlang.org/docs/handbook/declaration-files/templates/module-plugin-d-ts.html
-// - https://www.typescriptlang.org/docs/handbook/declaration-merging.html
-// - https://www.typescriptlang.org/docs/handbook/declaration-files/templates/global-plugin-d-ts.html
-// - https://www.typescriptlang.org/docs/handbook/declaration-files/templates/global-modifying-module-d-ts.html
-// - https://stackoverflow.com/questions/35074713/extending-typescript-global-object-in-node-js
-// - https://github.com/Microsoft/TypeScript/issues/15818
-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.spec.ts

@@ -1,101 +0,0 @@
-import {IDatabaseRepository} from './interface';
-import {NewPouchdbRepositoryWebWorker} from './pouchdb_repository';
-import {SourceType} from '../models/database/source_types';
-import {Source} from '../models/database/source';
-import {DocType} from './constants';
-import * as PouchDB from 'pouchdb/dist/pouchdb';
-import { v4 as uuidv4 } from 'uuid';
-import {PouchdbCrypto} from './plugins/crypto';
-
-describe('PouchdbRepository', () => {
-  let repository: IDatabaseRepository;
-
-  beforeEach(async () => {
-    let current_user = uuidv4() as string
-    let cryptoConfig = await PouchdbCrypto.CryptConfig(current_user, current_user)
-    await PouchdbCrypto.StoreCryptConfig(cryptoConfig)
-    repository = NewPouchdbRepositoryWebWorker({current_user: current_user, auth_token: ""}, '/database', new PouchDB("PouchdbRepository" + current_user));
-  });
-
-  afterEach(async () => {
-    if(repository){
-      const db = await repository.GetDB()
-      db.destroy() //wipe the db.
-    }
-  })
-
-
-  it('should be created', () => {
-    expect(repository).toBeTruthy();
-  });
-
-  describe('CreateSource', () => {
-    it('should return an id', async () => {
-      const createdId = await repository.UpsertSource(new Source({
-        patient: 'patient',
-        source_type: SourceType.Aetna,
-      }))
-
-      expect(createdId.totalResources).toEqual(1);
-      expect(createdId.updatedResources[0]).toEqual("source:aetna:patient");
-    });
-  })
-
-  describe('GetSource', () => {
-    it('should return an source', async () => {
-      const createdResource = await repository.UpsertSource(new Source({
-        patient: 'patient',
-        source_type: SourceType.Aetna,
-        access_token: 'hello-world',
-      }))
-
-      const createdSource = await repository.GetSource(createdResource.updatedResources[0])
-
-      expect(createdSource.doc_type).toEqual(DocType.Source);
-      expect(createdSource.patient).toEqual('patient');
-      expect(createdSource.source_type).toEqual(SourceType.Aetna);
-      expect(createdSource.access_token).toEqual('hello-world');
-    });
-  })
-
-  describe('DeleteSource', () => {
-    it('should delete a source', async () => {
-      const createdResource = await repository.UpsertSource(new Source({
-        patient: 'patient-to-delete',
-        source_type: SourceType.Aetna,
-        access_token: 'hello-world',
-      }))
-      console.log(createdResource)
-      const deletedSource = await repository.DeleteSource(createdResource.updatedResources[0])
-
-      expect(deletedSource).toBeTruthy();
-    });
-  })
-
-  describe('GetSources', () => {
-    it('should return a list of sources', async () => {
-      await repository.UpsertSource(new Source({
-        patient: 'patient1',
-        source_type: SourceType.Aetna,
-        access_token: 'hello-world1',
-      }))
-
-      await repository.UpsertSource(new Source({
-        patient: 'patient2',
-        source_type: SourceType.Aetna,
-        access_token: 'hello-world2',
-      }))
-
-      await repository.UpsertSource(new Source({
-        patient: 'patient3',
-        source_type: SourceType.Aetna,
-        access_token: 'hello-world3',
-      }))
-
-      const sourcesWrapped = await repository.GetSources()
-
-      expect(sourcesWrapped.total_rows).toEqual(3);
-      expect((sourcesWrapped.rows[0] as Source).patient).toEqual('patient1');
-    });
-  })
-});

frontend/src/lib/database/pouchdb_repository.ts

@@ -1,465 +0,0 @@
-import {Source} from '../models/database/source';
-import {IDatabasePaginatedResponse, IDatabaseDocument, IDatabaseRepository} from './interface';
-import {DocType} from './constants';
-import {ResourceFhir} from '../models/database/resource_fhir';
-import {ResourceTypeCounts, SourceSummary} from '../models/fasten/source-summary';
-import {Base64} from '../utils/base64';
-import {GetEndpointAbsolutePath} from '../utils/endpoint_absolute_path';
-
-// PouchDB & plugins
-import * as PouchDB from 'pouchdb/dist/pouchdb';
-
-// import * as PouchCrypto from 'crypto-pouch';
-// PouchDB.plugin(PouchCrypto);
-
-import * as PouchTransform from 'transform-pouch';
-PouchDB.plugin(PouchTransform);
-
-import {PouchdbUpsert} from './plugins/upsert';
-import {UpsertSummary} from '../models/fasten/upsert-summary';
-
-import {PouchdbCryptConfig, PouchdbCrypto, PouchdbCryptoOptions} from './plugins/crypto';
-import {utils} from 'protractor';
-
-// !!!!!!!!!!!!!!!!WARNING!!!!!!!!!!!!!!!!!!!!!
-// most pouchdb plugins seem to fail when used in a webworker.
-// !!!!!!!!!!!!!!!!WARNING!!!!!!!!!!!!!!!!!!!!!
-// import * as PouchUpsert from 'pouchdb-upsert';
-// PouchDB.plugin(PouchUpsert);
-// import find from 'pouchdb-find';
-// 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
-
-
-// this is required, otherwise PouchFind fails when looking for the global PouchDB variable
-
-/**
- * This method is used to initialize the repository from Workers.
- * Eventually this method should dyanmically dtermine the version of the repo to return from the env.
- * @constructor
- */
-
-export function NewPouchdbRepositoryWebWorker(auth: {current_user: string, auth_token: string}, couchDbEndpointBase: string, localPouchDb?: PouchDB.Database): PouchdbRepository {
-  let pouchdbRepository = new PouchdbRepository(couchDbEndpointBase, localPouchDb)
-  pouchdbRepository.current_user = auth.current_user
-  pouchdbRepository._auth_token = auth.auth_token
-  return pouchdbRepository
-}
-export class PouchdbRepository implements IDatabaseRepository {
-
-  // replicationHandler: any
-  remotePouchEndpoint: string // "http://localhost:5984"
-  pouchDb: PouchDB.Database
-  current_user: string
-  _auth_token: string
-
-  //encryption configuration
-  cryptConfig: PouchdbCryptConfig = null
-  encryptionInitComplete: boolean = false
-
-  // There are 3 different ways to initialize the Database
-  // - explicitly after signin/signup (not supported by this class, see FastenDbService)
-  // - explicitly during web-worker init
-  // - implicitly after Lighthouse redirect (not supported by this class, see FastenDbService)
-  // Three peices of information are required during intialization
-  // - couchdb endpoint (constant, see environment.couchdb_endpoint_base)
-  // - username
-  // - JWT token
-  constructor(couchDbEndpointBase: string, localPouchDb?: PouchDB.Database) {
-    // couchDbEndpointBase could be a relative or absolute path.
-    //if its absolute, we should pass it in, as-is
-    this.remotePouchEndpoint = GetEndpointAbsolutePath(globalThis.location, couchDbEndpointBase)
-
-
-    //setup PouchDB Plugins
-     //https://pouchdb.com/guides/mango-queries.html
-    this.pouchDb = null
-
-    if(localPouchDb){
-      console.warn("using local pouchdb, this should only be used for testing")
-      this.pouchDb = localPouchDb
-    }
-  }
-
-
-  // Teardown / deconfigure the existing database instance (if there is one).
-  // --
-  // CAUTION: Subsequent calls to .GetDB() will fail until a new instance is configured
-  // with a call to .ConfigureForUser().
-  public async Close(): Promise<void> {
-    if (!this.pouchDb) {
-      return;
-    }
-    // Stop remote replication for existing database
-    // if(this.replicationHandler){
-    //   this.replicationHandler.cancel()
-    // }
-
-    this.pouchDb.close();
-    this.pouchDb = null;
-    return
-  }
-
-
-  ///////////////////////////////////////////////////////////////////////////////////////
-  // Source
-
-  public async UpsertSource(source: Source): Promise<UpsertSummary> {
-    return this.upsertDocument(source);
-  }
-
-  public async GetSource(source_id: string): Promise<Source> {
-    return this.getDocument(source_id)
-      .then((doc) => {
-        return new Source(doc)
-      })
-  }
-
-  public async GetSources(): Promise<IDatabasePaginatedResponse> {
-    return this.findDocumentByDocType(DocType.Source)
-      .then((docWrapper) => {
-
-        docWrapper.rows = docWrapper.rows.map((result) => {
-          return new Source(result.doc)
-        })
-        return docWrapper
-      })
-  }
-
-  public async GetSourceSummary(source_id: string): Promise<SourceSummary> {
-    const sourceSummary = new SourceSummary()
-    sourceSummary.source = await this.GetSource(source_id)
-    sourceSummary.patient = await this.findDocumentByPrefix(`${DocType.ResourceFhir}:${Base64.Encode(source_id)}:Patient`, true)
-      .then((paginatedResp) => new ResourceFhir(paginatedResp?.rows[0].doc))
-
-    sourceSummary.resource_type_counts = await this.findDocumentByPrefix(`${DocType.ResourceFhir}:${Base64.Encode(source_id)}`, false)
-      .then((paginatedResp) => {
-        const lookup: {[name: string]: ResourceTypeCounts} = {}
-        paginatedResp?.rows.forEach((resourceWrapper) => {
-          const resourceIdParts = resourceWrapper.id.split(':')
-          const resourceType = resourceIdParts[2]
-
-          let currentResourceStats = lookup[resourceType] || {
-            count: 0,
-            source_id: Base64.Decode(resourceIdParts[1]),
-            resource_type: resourceType
-          }
-          currentResourceStats.count += 1
-          lookup[resourceType] = currentResourceStats
-        })
-
-        const arr = []
-        for(let key in lookup){
-          arr.push(lookup[key])
-        }
-        return arr
-      })
-    return sourceSummary
-  }
-
-  public async DeleteSource(source_id: string): Promise<boolean> {
-    return this.deleteDocument(source_id)
-  }
-
-  ///////////////////////////////////////////////////////////////////////////////////////
-  // Resource
-
-  public async UpsertResource(resource: ResourceFhir): Promise<UpsertSummary> {
-    return this.upsertDocument(resource);
-  }
-
-  public async UpsertResources(resources: ResourceFhir[]): Promise<UpsertSummary> {
-    return this.upsertBulk(resources);
-  }
-
-  public async GetResource(resource_id: string): Promise<ResourceFhir> {
-    return this.getDocument(resource_id)
-      .then((doc) => {
-        return new ResourceFhir(doc)
-      })
-  }
-
-  public async GetResources(): Promise<IDatabasePaginatedResponse> {
-    return this.findDocumentByDocType(DocType.ResourceFhir)
-      .then((docWrapper) => {
-
-        docWrapper.rows = docWrapper.rows.map((result) => {
-          return new ResourceFhir(result.doc)
-        })
-        return docWrapper
-      })
-  }
-
-  public async GetResourcesForSource(source_id: string, source_resource_type?: string): Promise<IDatabasePaginatedResponse> {
-    let prefix = `${DocType.ResourceFhir}:${Base64.Encode(source_id)}`
-    if(source_resource_type){
-      prefix += `:${source_resource_type}`
-    }
-
-    return this.findDocumentByPrefix(prefix, true)
-      .then((docWrapper) => {
-
-        docWrapper.rows = docWrapper.rows.map((result) => {
-          return new ResourceFhir(result.doc)
-        })
-        return docWrapper
-      })
-  }
-
-  /**
-   * given an raw connection to a database, determine how many records/resources are stored within
-   * @constructor
-   */
-  public async IsDatabasePopulated(): Promise<boolean> {
-    let resourceFhirCount = await this.findDocumentByPrefix(DocType.ResourceFhir, false, true)
-      .then((resp) => {
-        console.log("RESPONSE COUNT INFO", resp)
-        return resp.rows.length
-      })
-
-    if(resourceFhirCount > 0) {return true}
-
-
-    let sourceCount = await this.findDocumentByPrefix(DocType.Source, false, true)
-      .then((resp) => {
-        console.log("SOURCE COUNT INFO", resp)
-
-        return resp.rows.length
-      })
-    if(sourceCount > 0) {return true}
-
-    return false
-  }
-
-
-  ///////////////////////////////////////////////////////////////////////////////////////
-  // CRUD Operators
-  // All functions below here will return the raw PouchDB responses, and may need to be wrapped in
-  // new ResourceFhir(result.doc)
-  ///////////////////////////////////////////////////////////////////////////////////////
-  public ResetDB(){
-    this.pouchDb = null
-    this.encryptionInitComplete = false
-  }
-  // Get the active PouchDB instance. Throws an error if no PouchDB instance is
-  // available (ie, user has not yet been configured with call to .configureForUser()).
-  public async GetDB(skipEncryption: boolean = false): Promise<PouchDB.Database> {
-    await this.GetSessionDB()
-
-    if(!this.pouchDb) {
-      throw(new Error( "Database is not available - please configure an instance." ));
-    }
-
-    if(skipEncryption){
-      //this allows the database to be queried, even when encryption has not been configured correctly
-      //this will only be used to take a count of documents in the database, so we can prompt the user for a encryption key, or generate a new one (for an empty db)
-      return this.pouchDb
-    }
-
-
-    //try to determine the crypto configuration using the currently logged in user.
-    this.cryptConfig = await PouchdbCrypto.RetrieveCryptConfig(this.current_user)
-
-    if(!this.cryptConfig){
-      throw new Error("crypto configuration not set.")
-    }
-
-    if(!this.encryptionInitComplete){
-      return PouchdbCrypto.crypto(this.pouchDb, this.cryptConfig, {ignore:[
-          'doc_type',
-          'source_id',
-          'source_resource_type',
-          'source_resource_id',
-        ]})
-        .then((encryptedPouchDb) => {
-          this.pouchDb = encryptedPouchDb
-          this.encryptionInitComplete = true
-          return this.pouchDb
-        })
-    } else {
-      return this.pouchDb;
-    }
-  }
-
-
-  // update/insert a new document. Returns a promise of the generated id.
-  protected upsertDocument(newDoc: IDatabaseDocument) : Promise<UpsertSummary> {
-    // make sure we always "populate" the ID for every document before submitting
-    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) => {
-        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())
-            // console.log("merge, empty")
-            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 {
-            let errMsg = "unknown doc_type, cannot diff for upsert: " + newDoc.doc_type
-            console.error(errMsg)
-            throw new Error(errMsg)
-          }
-        })
-      })
-      .then(( result ): UpsertSummary => {
-        // // success, res is {rev: '1-xxx', updated: true, id: 'myDocId'}
-        const updateSummary = new UpsertSummary()
-        updateSummary.totalResources = 1
-
-        if(result.updated){
-            updateSummary.updatedResources = [result.id]
-        }
-        return updateSummary;
-      });
-  }
-
-  protected async upsertBulk(docs: IDatabaseDocument[]): Promise<UpsertSummary> {
-    //insert sequentially (not in parallel)
-    let finalUpsertSummary = new UpsertSummary()
-
-    for (let doc of docs){
-      doc.populateId();
-      let upsertSummary = await this.upsertDocument(doc)
-      finalUpsertSummary.totalResources += upsertSummary.totalResources
-      finalUpsertSummary.updatedResources = finalUpsertSummary.updatedResources.concat(upsertSummary.updatedResources)
-    }
-
-    return finalUpsertSummary
-  }
-
-  protected getDocument(id: string): Promise<any> {
-    return this.GetDB()
-      .then((db) => db.get(id))
-  }
-
-
-  protected findDocumentByDocType(docType: DocType, includeDocs: boolean = true): Promise<IDatabasePaginatedResponse> {
-    return this.findDocumentByPrefix(docType, includeDocs)
-  }
-  protected findDocumentByPrefix(prefix: string, includeDocs: boolean = true, skipEncryption: boolean = false): Promise<IDatabasePaginatedResponse> {
-    return this.GetDB(skipEncryption)
-      .then((db) => {
-        return db.allDocs({
-          include_docs: includeDocs,
-          startkey: `${prefix}:`,
-          endkey: `${prefix}:\uffff`
-        })
-      })
-
-  }
-
-  protected async deleteDocument(id: string): Promise<boolean> {
-    const docToDelete = await this.getDocument(id)
-    return this.GetDB()
-      .then((db) => db.remove(docToDelete))
-      .then((result) => {
-        return result.ok
-      })
-  }
-
-  ///////////////////////////////////////////////////////////////////////////////////////
-  // Sync private/protected methods
-  ///////////////////////////////////////////////////////////////////////////////////////
-  /**
-   * Try to get PouchDB database using session information
-   * This method is overridden in PouchDB Service, as session information is inaccessible in web-worker
-   * @constructor
-   */
-  public async GetSessionDB(): Promise<PouchDB.Database>  {
-    if(this.pouchDb){
-      console.log("Session DB already exists..")
-      return this.pouchDb
-    }
-
-    if(!this.current_user){
-      throw new Error("current user is required when initializing pouchdb within web-worker")
-    }
-    if(!this._auth_token){
-      throw new Error("auth token is required when initializing pouchdb within web-worker")
-    }
-    let auth_token = this._auth_token
-
-    // add JWT bearer token header to all requests
-    // https://stackoverflow.com/questions/62129654/how-to-handle-jwt-authentication-with-rxdb
-    this.pouchDb = new PouchDB(this.getRemoteUserDb(this.current_user), {
-      skip_setup: true,
-      fetch: function (url, opts) {
-        opts.headers.set('Authorization', `Bearer ${auth_token}`)
-        return PouchDB.fetch(url, opts);
-      }
-    })
-    return this.pouchDb
-  }
-
-  protected getRemoteUserDb(username: string){
-    return `${this.remotePouchEndpoint}/userdb-${this.toHex(username)}`
-  }
-  // protected enableSync(userIdentifier: string){
-  //   this.replicationHandler = this.localPouchDb.sync(this.getRemoteUserDb(userIdentifier), {live: true, retry: true})
-  //   return
-  // }
-
-
-  private toHex(s: string) {
-    // utf8 to latin1
-    s = unescape(encodeURIComponent(s))
-    let h = ''
-    for (let i = 0; i < s.length; i++) {
-      h += s.charCodeAt(i).toString(16)
-    }
-    return h
-  }
-}

frontend/src/lib/models/client/client-config.ts

@@ -1,6 +0,0 @@
-import {LighthouseSourceMetadata} from '../lighthouse/lighthouse-source-metadata';
-import {SourceType} from '../database/source_types';
-
-export class ClientConfig {
-  fasten_api_endpoint_base: string
-}

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

@@ -1,36 +0,0 @@
-import {DocType} from '../../database/constants';
-import {IResourceRaw} from '../../conduit/interface';
-import {Base64} from '../../utils/base64';
-
-export class ResourceFhir {
-  _id?: string
-  _rev?: string
-  doc_type: DocType = DocType.ResourceFhir
-  updated_at?: string
-
-  fhir_version: string = ""
-  source_id: string = ""
-  source_resource_type: string = ""
-  source_resource_id: string = ""
-
-  resource_raw?: IResourceRaw
-
-  constructor(object?: any) {
-    if(object){
-      object.doc_type = DocType.ResourceFhir
-      return Object.assign(this, object)
-    } else{
-      this.doc_type = DocType.ResourceFhir
-      return this
-    }
-  }
-
-  populateId(){
-    //TODO: source_id should be base64 encoded (otherwise we get nested : chars)
-    this._id = `${this.doc_type}:${Base64.Encode(this.source_id)}:${this.source_resource_type}:${this.source_resource_id}`
-  }
-  base64Id(): string {
-    this.populateId()
-    return Base64.Encode(this._id)
-  }
-}

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

@@ -1,32 +0,0 @@
-import {LighthouseSourceMetadata} from '../lighthouse/lighthouse-source-metadata';
-import {SourceType} from './source_types';
-import {DocType} from '../../../lib/database/constants';
-import {Base64} from '../../utils/base64';
-
-export class Source extends LighthouseSourceMetadata{
-  _id?: string
-  _rev?: string
-  doc_type: string
-  updated_at?: string
-
-  source_type: SourceType
-  patient: string
-  access_token:          string
-  refresh_token?:         string
-  id_token?:              string
-  expires_at:            number //seconds since epoch
-
-  constructor(object: any) {
-    super()
-    object.doc_type = DocType.Source
-    return Object.assign(this, object)
-  }
-
-  populateId(){
-    this._id = `${this.doc_type}:${this.source_type}:${this.patient}`
-  }
-  base64Id(): string {
-    this.populateId()
-    return Base64.Encode(this._id)
-  }
-}

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

@@ -1,50 +0,0 @@
-
-
-export enum SourceType {
-  Manual = "manual",
-
-  Athena    = "athena",
-  HealthIT  = "healthit",
-  Logica    = "logica",
-
-//platforms
-  CareEvolution  = "careevolution",
-  Cerner         = "cerner",
-  Epic           = "epic",
-
-//providers
-  Aetna                              = "aetna",
-  Amerigroup                         = "amerigroup",
-  AmerigroupMedicaid                 = "amerigroupmedicaid",
-  Anthem                             = "anthem",
-  AnthemBluecrossCA                  = "anthembluecrossca",
-  BlueButton                         = "bluebutton",
-  BluecrossBlueshieldKansasMedicare  = "bcbskansasmedicare",
-  BluecrossBlueshieldKansas          = "bcbskansas",
-  BluecrossBlueshieldNY              = "bcbsny",
-  BlueMedicareAdvantage              = "bluemedicareadvantage",
-  ClearHealthAlliance                = "clearhealthalliance",
-  Cigna                              = "cigna",
-  DellChildrens                      = "dellchildrens",
-  EmpireBlue                         = "empireblue",
-  EmpireBlueMedicaid                 = "empirebluemedicaid",
-  HealthyBlueLA                      = "healthybluela",
-  HealthyBlueLAMedicaid              = "healthybluelamedicaid",
-  HealthyBlueMO                      = "healthybluemo",
-  HealthyBlueMOMedicaid              = "healthybluemomedicaid",
-  HealthyBlueNC                      = "healthybluenc",
-  HealthyBlueNCMedicaid              = "healthybluencmedicaid",
-  HealthyBlueNE                      = "healthybluene",
-  HealthyBlueSC                      = "healthybluesc",
-  HighmarkWesternNY                  = "highmarkwesternny",
-  SimplyHealthcareMedicaid           = "simplyhealthcaremedicaid",
-  SimplyHealthcareMedicare           = "simplyhealthcaremedicare",
-  SummitCommunityCare                = "summitcommunitycare",
-  UCSF                               = "ucsf-health",
-  Unicare                            = "unicare",
-  UnicareMA                          = "unicarema",
-  UnicareMedicaid                    = "unicaremedicaid",
-  Humana                             = "humana",
-  Kaiser                             = "kaiser",
-  UnitedHealthcare                   = "unitedhealthcare",
-}