Merge pull request #7 from fastenhealth/spa

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Jason Kulatunga 2022-10-13 08:16:04 -07:00 committed by GitHub
commit 77c23e62f0
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216 changed files with 7046 additions and 233308 deletions

1
.gitignore vendored
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@ -57,3 +57,4 @@ fabric.properties
vendor
fasten.db
test.go
/.couchdb

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@ -4,4 +4,28 @@ cd frontend
npm run dist
go mod vendor
go run backend/cmd/fasten/fasten.go start --config ./config.example.yaml --debug
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
```
# Docker
``
- http://localhost:9090/web/dashboard - WebUI
- http://localhost:9090/database - CouchDB proxy
- http://localhost:5984/_utils/ - CouchDB admin UI
# Credentials
- Couchdb:
- username: `admin`
- password: `mysecretpassword`
- WebUI:
- username: `testuser`
- password: `testuser`
# Running tests
- ng test --include='**/base_client.spec.ts'
- ng test --include='lib/**/*.spec.ts'

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@ -1,3 +1,6 @@
#########################################################################################################
# Frontend Build
#########################################################################################################
FROM node:18.9.0 as frontend-build
WORKDIR /usr/src/fastenhealth/frontend
#COPY frontend/package.json frontend/yarn.lock ./
@ -8,6 +11,9 @@ RUN yarn config set registry "http://registry.npmjs.org" \
COPY frontend/ ./
RUN yarn run build -- --configuration sandbox --output-path=../dist
#########################################################################################################
# Backend Build
#########################################################################################################
FROM golang:1.18 as backend-build
WORKDIR /go/src/github.com/fastenhealth/fastenhealth-onprem
COPY . .
@ -26,12 +32,29 @@ RUN mkdir -p /opt/fasten/db \
&& curl -o /opt/fasten/db/fasten.db -L https://github.com/fastenhealth/testdata/raw/main/fasten.db
#########################################################################################################
# Distribution Build
#########################################################################################################
FROM couchdb:3.2
ARG S6_ARCH=amd64
RUN curl https://github.com/just-containers/s6-overlay/releases/download/v1.21.8.0/s6-overlay-${S6_ARCH}.tar.gz -L -s --output /tmp/s6-overlay-${S6_ARCH}.tar.gz \
&& tar xzf /tmp/s6-overlay-${S6_ARCH}.tar.gz -C / \
&& rm -rf /tmp/s6-overlay-${S6_ARCH}.tar.gz
COPY /docker/couchdb/local.ini /opt/couchdb/etc/
COPY /docker/rootfs /
FROM gcr.io/distroless/static-debian11
WORKDIR /opt/fasten/
COPY --from=backend-build /opt/fasten/ /opt/fasten/
COPY --from=frontend-build /usr/src/fastenhealth/dist /opt/fasten/web
COPY --from=backend-build /go/bin/fasten /opt/fasten/fasten
COPY LICENSE.md /opt/fasten/LICENSE.md
COPY config.yaml /opt/fasten/config/config.yaml
CMD ["/opt/fasten/fasten", "start", "--config", "/opt/fasten/config/config.yaml"]
ENTRYPOINT ["/init"]

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@ -1,15 +1,674 @@
Copyright (C) Jason Kulatunga - All Rights Reserved.
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permissions. However, no additional obligations are imposed on any
author or copyright holder as a result of your choosing to follow a
later version.
15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. Limitation of Liability.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
<program> Copyright (C) <year> <name of author>
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<https://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<https://www.gnu.org/licenses/why-not-lgpl.html>.

View File

@ -6,3 +6,4 @@ Find & replace the following
- `fastenhealth` - find and replace this with your binary name
- make sure you rename the folder as well.

View File

@ -1,56 +0,0 @@
package auth
import (
"errors"
"github.com/golang-jwt/jwt"
"time"
)
//TODO: this should match the ID and username for the user.
type JWTClaim struct {
Username string `json:"username"`
UserId string `json:"user_id"`
Email string `json:"email"`
jwt.StandardClaims
}
func GenerateJWT(encryptionKey string, username string, userId string) (tokenString string, err error) {
expirationTime := time.Now().Add(2 * time.Hour)
claims := &JWTClaim{
Username: username,
Email: username,
UserId: userId,
StandardClaims: jwt.StandardClaims{
ExpiresAt: expirationTime.Unix(),
},
}
token := jwt.NewWithClaims(jwt.SigningMethodHS256, claims)
tokenString, err = token.SignedString([]byte(encryptionKey))
return
}
func ValidateToken(encryptionKey string, signedToken string) (*JWTClaim, error) {
token, err := jwt.ParseWithClaims(
signedToken,
&JWTClaim{},
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.(*JWTClaim)
if !ok {
err = errors.New("couldn't parse claims")
return nil, err
}
if claims.ExpiresAt < time.Now().Local().Unix() {
err = errors.New("token expired")
return nil, err
}
return claims, nil
}

View File

@ -25,7 +25,12 @@ func (c *configuration) Init() error {
c.SetDefault("web.listen.host", "0.0.0.0")
c.SetDefault("web.listen.basepath", "")
c.SetDefault("web.src.frontend.path", "/opt/fasten/web")
c.SetDefault("web.database.location", "/opt/fasten/db/fasten.db") //TODO: should be /opt/fasten/fasten.db
c.SetDefault("web.couchdb.scheme", "http")
c.SetDefault("web.couchdb.host", "localhost")
c.SetDefault("web.couchdb.port", "5984")
c.SetDefault("web.couchdb.admin_username", "admin")
c.SetDefault("web.couchdb.admin_password", "mysecretpassword")
c.SetDefault("log.level", "INFO")
c.SetDefault("log.file", "")
@ -72,9 +77,5 @@ func (c *configuration) ReadConfig(configFilePath string) error {
// This function ensures that required configuration keys (that must be manually set) are present
func (c *configuration) ValidateConfig() error {
if !c.IsSet("web.jwt.encryptionkey") {
return errors.ConfigValidationError("`web.jwt.encryptionkey` configuration option must be set")
}
return nil
}

View File

@ -0,0 +1,77 @@
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"
)
func NewRepository(appConfig config.Interface, globalLogger logrus.FieldLogger) (DatabaseRepository, error) {
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// Couchdb setup
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
couchdbUrl := fmt.Sprintf("%s://%s:%s", appConfig.GetString("web.couchdb.scheme"), appConfig.GetString("web.couchdb.host"), appConfig.GetString("web.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("web.couchdb.admin_username"),
appConfig.GetString("web.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"`
}
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,
}
db := cr.client.DB(ctx, "_users")
_, err := db.Put(ctx, newUser.ID, newUser)
return err
}
func (cr *couchdbRepository) Close() error {
return nil
}

View File

@ -10,21 +10,4 @@ type DatabaseRepository interface {
Close() error
CreateUser(context.Context, *models.User) error
GetUserByEmail(context.Context, string) (*models.User, error)
GetCurrentUser(context.Context) *models.User
GetSummary(ctx context.Context) (*models.Summary, error)
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)
//UpsertProfile(context.Context, *models.Profile) error
//UpsertOrganziation(context.Context, *models.Organization) error
CreateSource(context.Context, *models.Source) error
GetSource(context.Context, string) (*models.Source, error)
GetSourceSummary(context.Context, string) (*models.SourceSummary, error)
GetSources(context.Context) ([]models.Source, error)
}

View File

@ -49,20 +49,6 @@ func (mr *MockDatabaseRepositoryMockRecorder) Close() *gomock.Call {
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "Close", reflect.TypeOf((*MockDatabaseRepository)(nil).Close))
}
// CreateSource mocks base method.
func (m *MockDatabaseRepository) CreateSource(arg0 context.Context, arg1 *models.Source) error {
m.ctrl.T.Helper()
ret := m.ctrl.Call(m, "CreateSource", arg0, arg1)
ret0, _ := ret[0].(error)
return ret0
}
// CreateSource indicates an expected call of CreateSource.
func (mr *MockDatabaseRepositoryMockRecorder) CreateSource(arg0, arg1 interface{}) *gomock.Call {
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "CreateSource", reflect.TypeOf((*MockDatabaseRepository)(nil).CreateSource), arg0, arg1)
}
// CreateUser mocks base method.
func (m *MockDatabaseRepository) CreateUser(arg0 context.Context, arg1 *models.User) error {
m.ctrl.T.Helper()
@ -76,166 +62,3 @@ func (mr *MockDatabaseRepositoryMockRecorder) CreateUser(arg0, arg1 interface{})
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "CreateUser", reflect.TypeOf((*MockDatabaseRepository)(nil).CreateUser), arg0, arg1)
}
// GetCurrentUser mocks base method.
func (m *MockDatabaseRepository) GetCurrentUser(arg0 context.Context) models.User {
m.ctrl.T.Helper()
ret := m.ctrl.Call(m, "GetCurrentUser", arg0)
ret0, _ := ret[0].(models.User)
return ret0
}
// GetCurrentUser indicates an expected call of GetCurrentUser.
func (mr *MockDatabaseRepositoryMockRecorder) GetCurrentUser(arg0 interface{}) *gomock.Call {
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "GetCurrentUser", reflect.TypeOf((*MockDatabaseRepository)(nil).GetCurrentUser), arg0)
}
// GetPatientForSources mocks base method.
func (m *MockDatabaseRepository) GetPatientForSources(ctx context.Context) ([]models.ResourceFhir, error) {
m.ctrl.T.Helper()
ret := m.ctrl.Call(m, "GetPatientForSources", ctx)
ret0, _ := ret[0].([]models.ResourceFhir)
ret1, _ := ret[1].(error)
return ret0, ret1
}
// GetPatientForSources indicates an expected call of GetPatientForSources.
func (mr *MockDatabaseRepositoryMockRecorder) GetPatientForSources(ctx interface{}) *gomock.Call {
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "GetPatientForSources", reflect.TypeOf((*MockDatabaseRepository)(nil).GetPatientForSources), ctx)
}
// GetResource mocks base method.
func (m *MockDatabaseRepository) GetResource(arg0 context.Context, arg1 string) (*models.ResourceFhir, error) {
m.ctrl.T.Helper()
ret := m.ctrl.Call(m, "GetResource", arg0, arg1)
ret0, _ := ret[0].(*models.ResourceFhir)
ret1, _ := ret[1].(error)
return ret0, ret1
}
// GetResource indicates an expected call of GetResource.
func (mr *MockDatabaseRepositoryMockRecorder) GetResource(arg0, arg1 interface{}) *gomock.Call {
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "GetResource", reflect.TypeOf((*MockDatabaseRepository)(nil).GetResource), arg0, arg1)
}
// GetResourceBySourceId mocks base method.
func (m *MockDatabaseRepository) GetResourceBySourceId(arg0 context.Context, arg1, arg2 string) (*models.ResourceFhir, error) {
m.ctrl.T.Helper()
ret := m.ctrl.Call(m, "GetResourceBySourceId", arg0, arg1, arg2)
ret0, _ := ret[0].(*models.ResourceFhir)
ret1, _ := ret[1].(error)
return ret0, ret1
}
// GetResourceBySourceId indicates an expected call of GetResourceBySourceId.
func (mr *MockDatabaseRepositoryMockRecorder) GetResourceBySourceId(arg0, arg1, arg2 interface{}) *gomock.Call {
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "GetResourceBySourceId", reflect.TypeOf((*MockDatabaseRepository)(nil).GetResourceBySourceId), arg0, arg1, arg2)
}
// GetSource mocks base method.
func (m *MockDatabaseRepository) GetSource(arg0 context.Context, arg1 string) (*models.Source, error) {
m.ctrl.T.Helper()
ret := m.ctrl.Call(m, "GetSource", arg0, arg1)
ret0, _ := ret[0].(*models.Source)
ret1, _ := ret[1].(error)
return ret0, ret1
}
// GetSource indicates an expected call of GetSource.
func (mr *MockDatabaseRepositoryMockRecorder) GetSource(arg0, arg1 interface{}) *gomock.Call {
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "GetSource", reflect.TypeOf((*MockDatabaseRepository)(nil).GetSource), arg0, arg1)
}
// GetSourceSummary mocks base method.
func (m *MockDatabaseRepository) GetSourceSummary(arg0 context.Context, arg1 string) (*models.SourceSummary, error) {
m.ctrl.T.Helper()
ret := m.ctrl.Call(m, "GetSourceSummary", arg0, arg1)
ret0, _ := ret[0].(*models.SourceSummary)
ret1, _ := ret[1].(error)
return ret0, ret1
}
// GetSourceSummary indicates an expected call of GetSourceSummary.
func (mr *MockDatabaseRepositoryMockRecorder) GetSourceSummary(arg0, arg1 interface{}) *gomock.Call {
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "GetSourceSummary", reflect.TypeOf((*MockDatabaseRepository)(nil).GetSourceSummary), arg0, arg1)
}
// GetSources mocks base method.
func (m *MockDatabaseRepository) GetSources(arg0 context.Context) ([]models.Source, error) {
m.ctrl.T.Helper()
ret := m.ctrl.Call(m, "GetSources", arg0)
ret0, _ := ret[0].([]models.Source)
ret1, _ := ret[1].(error)
return ret0, ret1
}
// GetSources indicates an expected call of GetSources.
func (mr *MockDatabaseRepositoryMockRecorder) GetSources(arg0 interface{}) *gomock.Call {
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "GetSources", reflect.TypeOf((*MockDatabaseRepository)(nil).GetSources), arg0)
}
// GetSummary mocks base method.
func (m *MockDatabaseRepository) GetSummary(ctx context.Context) (*models.Summary, error) {
m.ctrl.T.Helper()
ret := m.ctrl.Call(m, "GetSummary", ctx)
ret0, _ := ret[0].(*models.Summary)
ret1, _ := ret[1].(error)
return ret0, ret1
}
// GetSummary indicates an expected call of GetSummary.
func (mr *MockDatabaseRepositoryMockRecorder) GetSummary(ctx interface{}) *gomock.Call {
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "GetSummary", reflect.TypeOf((*MockDatabaseRepository)(nil).GetSummary), ctx)
}
// GetUserByEmail mocks base method.
func (m *MockDatabaseRepository) GetUserByEmail(arg0 context.Context, arg1 string) (*models.User, error) {
m.ctrl.T.Helper()
ret := m.ctrl.Call(m, "GetUserByEmail", arg0, arg1)
ret0, _ := ret[0].(*models.User)
ret1, _ := ret[1].(error)
return ret0, ret1
}
// GetUserByEmail indicates an expected call of GetUserByEmail.
func (mr *MockDatabaseRepositoryMockRecorder) GetUserByEmail(arg0, arg1 interface{}) *gomock.Call {
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "GetUserByEmail", reflect.TypeOf((*MockDatabaseRepository)(nil).GetUserByEmail), arg0, arg1)
}
// ListResources mocks base method.
func (m *MockDatabaseRepository) ListResources(arg0 context.Context, arg1 models.ListResourceQueryOptions) ([]models.ResourceFhir, error) {
m.ctrl.T.Helper()
ret := m.ctrl.Call(m, "ListResources", arg0, arg1)
ret0, _ := ret[0].([]models.ResourceFhir)
ret1, _ := ret[1].(error)
return ret0, ret1
}
// ListResources indicates an expected call of ListResources.
func (mr *MockDatabaseRepositoryMockRecorder) ListResources(arg0, arg1 interface{}) *gomock.Call {
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "ListResources", reflect.TypeOf((*MockDatabaseRepository)(nil).ListResources), arg0, arg1)
}
// UpsertResource mocks base method.
func (m *MockDatabaseRepository) UpsertResource(arg0 context.Context, arg1 models.ResourceFhir) error {
m.ctrl.T.Helper()
ret := m.ctrl.Call(m, "UpsertResource", arg0, arg1)
ret0, _ := ret[0].(error)
return ret0
}
// UpsertResource indicates an expected call of UpsertResource.
func (mr *MockDatabaseRepositoryMockRecorder) UpsertResource(arg0, arg1 interface{}) *gomock.Call {
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "UpsertResource", reflect.TypeOf((*MockDatabaseRepository)(nil).UpsertResource), arg0, arg1)
}

View File

@ -1,378 +0,0 @@
package database
import (
"context"
"encoding/json"
"fmt"
"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/gorm"
"net/url"
)
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("web.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("web.database.location")+pragmaStr), &gorm.Config{
//TODO: figure out how to log database queries again.
//Logger: logger
DisableForeignKeyConstraintWhenMigrating: true,
})
if err != nil {
return nil, fmt.Errorf("Failed to connect to database! - %v", err)
}
globalLogger.Infof("Successfully connected to scrutiny sqlite db: %s\n", appConfig.GetString("web.database.location"))
//TODO: automigrate for now
err = database.AutoMigrate(
&models.User{},
&models.Source{},
&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
}
summary := &models.Summary{
Sources: sources,
ResourceTypeCounts: resourceCountResults,
Patients: patients,
}
return summary, nil
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// Resource
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
func (sr *sqliteRepository) UpsertResource(ctx context.Context, resourceModel *models.ResourceFhir) error {
sr.logger.Infof("insert/update (%T) %v", resourceModel, resourceModel)
if sr.gormClient.Debug().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.Debug().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.Source
//results := sr.gormClient.WithContext(ctx).
// Where(models.Source{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
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// Source
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
func (sr *sqliteRepository) CreateSource(ctx context.Context, sourceCreds *models.Source) error {
sourceCreds.UserID = sr.GetCurrentUser(ctx).ID
if sr.gormClient.WithContext(ctx).
Where(models.Source{
UserID: sourceCreds.UserID,
SourceType: sourceCreds.SourceType,
PatientId: sourceCreds.PatientId}).Updates(sourceCreds).RowsAffected == 0 {
return sr.gormClient.WithContext(ctx).Create(sourceCreds).Error
}
return nil
}
func (sr *sqliteRepository) GetSource(ctx context.Context, sourceId string) (*models.Source, error) {
sourceUUID, err := uuid.Parse(sourceId)
if err != nil {
return nil, err
}
var sourceCred models.Source
results := sr.gormClient.WithContext(ctx).
Where(models.Source{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.Source, error) {
var sourceCreds []models.Source
results := sr.gormClient.WithContext(ctx).
Where(models.Source{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 ""
}

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@ -1,12 +0,0 @@
# Hub
The Fasten Hub is a semi stand-alone application that can retrieve data from various Medical Providers, transform it, and
store it in the database. This code will eventually be moved into its own repository.
# Types
There are multiple protocols used by the Medical Provider industry to transfer patient data, the following mechanisms are the
ones that Fasten supports
### FHIR

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@ -1,58 +0,0 @@
package hub
import (
"context"
"errors"
"fmt"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/aetna"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/athena"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/base"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/bluebutton"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/careevolution"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/cerner"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/cigna"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/epic"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/healthit"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/logica"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/manual"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
"github.com/sirupsen/logrus"
"net/http"
)
func NewClient(sourceType pkg.SourceType, ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, credentials models.Source, testHttpClient ...*http.Client) (base.Client, *models.Source, error) {
var sourceClient base.Client
var updatedSource *models.Source
var err error
switch sourceType {
case pkg.SourceTypeAetna:
sourceClient, updatedSource, err = aetna.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
case pkg.SourceTypeAthena:
sourceClient, updatedSource, err = athena.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
case pkg.SourceTypeAnthem:
sourceClient, updatedSource, err = cigna.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
case pkg.SourceTypeBlueButtonMedicare:
sourceClient, updatedSource, err = bluebutton.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
case pkg.SourceTypeCareEvolution:
sourceClient, updatedSource, err = careevolution.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
case pkg.SourceTypeCerner:
sourceClient, updatedSource, err = cerner.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
case pkg.SourceTypeCigna:
sourceClient, updatedSource, err = cigna.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
case pkg.SourceTypeEpic:
sourceClient, updatedSource, err = epic.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
case pkg.SourceTypeHealthIT:
sourceClient, updatedSource, err = healthit.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
case pkg.SourceTypeLogica:
sourceClient, updatedSource, err = logica.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
case pkg.SourceTypeManual:
sourceClient, updatedSource, err = manual.NewClient(ctx, appConfig, globalLogger, credentials, testHttpClient...)
default:
return nil, updatedSource, errors.New(fmt.Sprintf("Unknown Source Type: %s", sourceType))
}
return sourceClient, updatedSource, err
}

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@ -1,49 +0,0 @@
package aetna
import (
"context"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/base"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
"github.com/sirupsen/logrus"
"net/http"
)
type AetnaClient struct {
*base.FHIR401Client
}
func NewClient(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (base.Client, *models.Source, error) {
baseClient, updatedSource, err := base.NewFHIR401Client(ctx, appConfig, globalLogger, source, testHttpClient...)
return AetnaClient{
baseClient,
}, updatedSource, err
}
//Overrides
func (c AetnaClient) SyncAll(db database.DatabaseRepository) error {
bundle, err := c.GetResourceBundle("Patient")
if err != nil {
c.Logger.Infof("An error occurred while getting patient bundle %s", c.Source.PatientId)
return err
}
wrappedResourceModels, err := c.ProcessBundle(bundle)
if err != nil {
c.Logger.Infof("An error occurred while processing patient bundle %s", c.Source.PatientId)
return err
}
//todo, create the resources in dependency order
for _, apiModel := range wrappedResourceModels {
err = db.UpsertResource(context.Background(), &apiModel)
if err != nil {
c.Logger.Info("An error occurred while upserting resource")
return err
}
}
return nil
}

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@ -1,49 +0,0 @@
package athena
import (
"context"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/base"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
"github.com/sirupsen/logrus"
"net/http"
)
type AthenaClient struct {
*base.FHIR401Client
}
func NewClient(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (base.Client, *models.Source, error) {
baseClient, updatedSource, err := base.NewFHIR401Client(ctx, appConfig, globalLogger, source, testHttpClient...)
return AthenaClient{
baseClient,
}, updatedSource, err
}
func (c AthenaClient) SyncAll(db database.DatabaseRepository) error {
supportedResources := []string{
"AllergyIntolerance",
//"Binary",
"CarePlan",
"CareTeam",
"Condition",
"Device",
"DiagnosticReport",
"DocumentReference",
"Encounter",
"Goal",
"Immunization",
//"Location",
//"Medication",
//"MedicationRequest",
"Observation",
//"Organization",
//"Patient",
//"Practitioner",
"Procedure",
//"Provenance",
}
return c.SyncAllByResourceName(db, supportedResources)
}

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@ -1,154 +0,0 @@
package base
import (
"context"
"encoding/json"
"fmt"
"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/sirupsen/logrus"
"golang.org/x/oauth2"
"io"
"log"
"net/http"
"net/url"
"os"
"strings"
"time"
)
type BaseClient struct {
Context context.Context
AppConfig config.Interface
Logger logrus.FieldLogger
OauthClient *http.Client
Source models.Source
Headers map[string]string
}
func (c *BaseClient) SyncAllBundle(db database.DatabaseRepository, bundleFile *os.File) error {
panic("SyncAllBundle functionality is not available on this client")
}
func NewBaseClient(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (*BaseClient, *models.Source, error) {
var httpClient *http.Client
var updatedSource *models.Source
if len(testHttpClient) == 0 {
//check if we need to refresh the access token
//https://github.com/golang/oauth2/issues/84#issuecomment-520099526
// https://chromium.googlesource.com/external/github.com/golang/oauth2/+/8f816d62a2652f705144857bbbcc26f2c166af9e/oauth2.go#239
conf := &oauth2.Config{
ClientID: source.ClientId,
ClientSecret: "",
Endpoint: oauth2.Endpoint{
AuthURL: source.OauthAuthorizationEndpoint,
TokenURL: source.OauthTokenEndpoint,
},
//RedirectURL: "",
//Scopes: nil,
}
token := &oauth2.Token{
TokenType: "Bearer",
RefreshToken: source.RefreshToken,
AccessToken: source.AccessToken,
Expiry: time.Unix(source.ExpiresAt, 0),
}
if token.Expiry.Before(time.Now()) { // expired so let's update it
log.Println("access token expired, refreshing...")
src := conf.TokenSource(ctx, token)
newToken, err := src.Token() // this actually goes and renews the tokens
if err != nil {
return nil, nil, err
}
if newToken.AccessToken != token.AccessToken {
token = newToken
// update the "source" credential with new data (which will need to be sent
updatedSource = &source
updatedSource.AccessToken = newToken.AccessToken
updatedSource.ExpiresAt = newToken.Expiry.Unix()
// Don't overwrite `RefreshToken` with an empty value
// if this was a token refreshing request.
if newToken.RefreshToken != "" {
updatedSource.RefreshToken = newToken.RefreshToken
}
}
}
// OLD CODE
httpClient = oauth2.NewClient(ctx, oauth2.StaticTokenSource(token))
} else {
//Testing mode.
httpClient = testHttpClient[0]
}
httpClient.Timeout = 10 * time.Second
return &BaseClient{
Context: ctx,
AppConfig: appConfig,
Logger: globalLogger,
OauthClient: httpClient,
Source: source,
Headers: map[string]string{},
}, updatedSource, nil
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// HttpClient
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
func (c *BaseClient) GetRequest(resourceSubpathOrNext string, decodeModelPtr interface{}) error {
resourceUrl, err := url.Parse(resourceSubpathOrNext)
if err != nil {
return err
}
if !resourceUrl.IsAbs() {
resourceUrl, err = url.Parse(fmt.Sprintf("%s/%s", strings.TrimRight(c.Source.ApiEndpointBaseUrl, "/"), strings.TrimLeft(resourceSubpathOrNext, "/")))
}
if err != nil {
return err
}
req, err := http.NewRequest(http.MethodGet, resourceUrl.String(), nil)
if err != nil {
return err
}
for key, val := range c.Headers {
//req.Header.Add("Accept", "application/json+fhir")
req.Header.Add(key, val)
}
//resp, err := c.OauthClient.Get(url)
resp, err := c.OauthClient.Do(req)
if err != nil {
return err
}
defer resp.Body.Close()
if resp.StatusCode >= 300 || resp.StatusCode < 200 {
b, _ := io.ReadAll(resp.Body)
return fmt.Errorf("An error occurred during request %s - %d - %s [%s]", resourceUrl, resp.StatusCode, resp.Status, string(b))
}
err = ParseBundle(resp.Body, decodeModelPtr)
return err
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// Helper Functions
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
func ParseBundle(r io.Reader, decodeModelPtr interface{}) error {
decoder := json.NewDecoder(r)
//decoder.DisallowUnknownFields() //make sure we throw an error if unknown fields are present.
err := decoder.Decode(decodeModelPtr)
if err != nil {
return err
}
return err
}

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@ -1,208 +0,0 @@
package base
import (
"context"
"fmt"
"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/fastenhealth/gofhir-models/fhir401"
fhirutils "github.com/fastenhealth/gofhir-models/fhir401/utils"
"github.com/samber/lo"
"github.com/sirupsen/logrus"
"gorm.io/datatypes"
"net/http"
)
type FHIR401Client struct {
*BaseClient
}
func NewFHIR401Client(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (*FHIR401Client, *models.Source, error) {
baseClient, updatedSource, err := NewBaseClient(ctx, appConfig, globalLogger, source, testHttpClient...)
return &FHIR401Client{
baseClient,
}, updatedSource, err
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// Sync
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
func (c *FHIR401Client) SyncAll(db database.DatabaseRepository) error {
bundle, err := c.GetPatientBundle(c.Source.PatientId)
if err != nil {
return err
}
wrappedResourceModels, err := c.ProcessBundle(bundle)
if err != nil {
c.Logger.Infof("An error occurred while processing patient bundle %s", c.Source.PatientId)
return err
}
//todo, create the resources in dependency order
for _, apiModel := range wrappedResourceModels {
err = db.UpsertResource(context.Background(), &apiModel)
if err != nil {
return err
}
}
return nil
}
//TODO, find a way to sync references that cannot be searched by patient ID.
func (c *FHIR401Client) SyncAllByResourceName(db database.DatabaseRepository, resourceNames []string) error {
//Store the Patient
patientResource, err := c.GetPatient(c.Source.PatientId)
if err != nil {
return err
}
patientJson, err := patientResource.MarshalJSON()
if err != nil {
return err
}
patientResourceType, patientResourceId := patientResource.ResourceRef()
patientResourceFhir := models.ResourceFhir{
OriginBase: models.OriginBase{
UserID: c.Source.UserID,
SourceID: c.Source.ID,
SourceResourceType: patientResourceType,
SourceResourceID: *patientResourceId,
},
Payload: datatypes.JSON(patientJson),
}
db.UpsertResource(context.Background(), &patientResourceFhir)
//error map storage.
syncErrors := map[string]error{}
//Store all other resources.
for _, resourceType := range resourceNames {
bundle, err := c.GetResourceBundle(fmt.Sprintf("%s?patient=%s", resourceType, c.Source.PatientId))
if err != nil {
syncErrors[resourceType] = err
continue
}
wrappedResourceModels, err := c.ProcessBundle(bundle)
if err != nil {
c.Logger.Infof("An error occurred while processing %s bundle %s", resourceType, c.Source.PatientId)
syncErrors[resourceType] = err
continue
}
for _, apiModel := range wrappedResourceModels {
err = db.UpsertResource(context.Background(), &apiModel)
if err != nil {
syncErrors[resourceType] = err
continue
}
}
}
if len(syncErrors) > 0 {
return fmt.Errorf("%d error(s) occurred during sync: %v", len(syncErrors), syncErrors)
}
return nil
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// FHIR
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
func (c *FHIR401Client) GetResourceBundle(relativeResourcePath string) (fhir401.Bundle, error) {
// https://www.hl7.org/fhir/patient-operation-everything.html
bundle := fhir401.Bundle{}
err := c.GetRequest(relativeResourcePath, &bundle)
if err != nil {
return bundle, err
}
var next string
var prev string
var self string
for _, link := range 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
}
}
for len(next) > 0 && next != self && next != prev {
c.Logger.Debugf("Paginated request => %s", next)
nextBundle := fhir401.Bundle{}
err := c.GetRequest(next, &nextBundle)
if err != nil {
return bundle, nil //ignore failures when paginating?
}
bundle.Entry = append(bundle.Entry, nextBundle.Entry...)
next = "" //reset the pointers
self = ""
prev = ""
for _, link := range 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, err
}
func (c *FHIR401Client) GetPatientBundle(patientId string) (fhir401.Bundle, error) {
return c.GetResourceBundle(fmt.Sprintf("Patient/%s/$everything", patientId))
}
func (c *FHIR401Client) GetPatient(patientId string) (fhir401.Patient, error) {
patient := fhir401.Patient{}
err := c.GetRequest(fmt.Sprintf("Patient/%s", patientId), &patient)
return patient, err
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// Process Bundles
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
func (c *FHIR401Client) ProcessBundle(bundle fhir401.Bundle) ([]models.ResourceFhir, error) {
//process each entry in bundle
wrappedResourceModels := lo.FilterMap[fhir401.BundleEntry, models.ResourceFhir](bundle.Entry, func(bundleEntry fhir401.BundleEntry, _ int) (models.ResourceFhir, bool) {
originalResource, _ := fhirutils.MapToResource(bundleEntry.Resource, false)
resourceType, resourceId := originalResource.(ResourceInterface).ResourceRef()
// TODO find a way to safely/consistently get the resource updated date (and other metadata) which shoudl be added to the model.
//if originalResource.Meta != nil && originalResource.Meta.LastUpdated != nil {
// if parsed, err := time.Parse(time.RFC3339Nano, *originalResource.Meta.LastUpdated); err == nil {
// patientProfile.UpdatedAt = parsed
// }
//}
if resourceId == nil {
//no resourceId present for this resource, we'll ignore it.
return models.ResourceFhir{}, false
}
wrappedResourceModel := models.ResourceFhir{
OriginBase: models.OriginBase{
ModelBase: models.ModelBase{},
UserID: c.Source.UserID,
SourceID: c.Source.ID,
SourceResourceID: *resourceId,
SourceResourceType: resourceType,
},
Payload: datatypes.JSON(bundleEntry.Resource),
}
return wrappedResourceModel, true
})
return wrappedResourceModels, nil
}

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@ -1,80 +0,0 @@
package base
import (
"context"
"encoding/json"
mock_config "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config/mock"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
"github.com/fastenhealth/gofhir-models/fhir401"
"github.com/golang/mock/gomock"
"github.com/sirupsen/logrus"
"github.com/stretchr/testify/require"
"io/ioutil"
"net/http"
"os"
"testing"
)
// helpers
func readTestFixture(path string) ([]byte, error) {
jsonFile, err := os.Open(path)
if err != nil {
return nil, err
}
defer jsonFile.Close()
return ioutil.ReadAll(jsonFile)
}
func TestNewFHIR401Client(t *testing.T) {
t.Parallel()
//setup
mockCtrl := gomock.NewController(t)
defer mockCtrl.Finish()
fakeConfig := mock_config.NewMockInterface(mockCtrl)
testLogger := logrus.WithFields(logrus.Fields{
"type": "test",
})
//test
client, _, err := NewFHIR401Client(context.Background(), fakeConfig, testLogger, models.Source{
RefreshToken: "test-refresh-token",
AccessToken: "test-access-token",
}, &http.Client{})
//assert
require.NoError(t, err)
require.Equal(t, client.Source.AccessToken, "test-access-token")
require.Equal(t, client.Source.RefreshToken, "test-refresh-token")
}
func TestFHIR401Client_ProcessBundle(t *testing.T) {
t.Parallel()
//setup
mockCtrl := gomock.NewController(t)
defer mockCtrl.Finish()
fakeConfig := mock_config.NewMockInterface(mockCtrl)
testLogger := logrus.WithFields(logrus.Fields{
"type": "test",
})
client, _, err := NewFHIR401Client(context.Background(), fakeConfig, testLogger, models.Source{
RefreshToken: "test-refresh-token",
AccessToken: "test-access-token",
}, &http.Client{})
require.NoError(t, err)
jsonBytes, err := readTestFixture("testdata/fixtures/401-R4/bundle/cigna_syntheticuser05-everything.json")
require.NoError(t, err)
var bundle fhir401.Bundle
err = json.Unmarshal(jsonBytes, &bundle)
require.NoError(t, err)
// test
wrappedResourceModels, err := client.ProcessBundle(bundle)
//log.Printf("%v", wrappedResourceModels)
//assert
require.NoError(t, err)
require.Equal(t, 11, len(wrappedResourceModels))
//require.Equal(t, "A00000000000005", profile.SourceResourceID)
}

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@ -1,81 +0,0 @@
package base
import (
"context"
"fmt"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
"github.com/fastenhealth/gofhir-models/fhir430"
fhirutils "github.com/fastenhealth/gofhir-models/fhir430/utils"
"github.com/samber/lo"
"github.com/sirupsen/logrus"
"gorm.io/datatypes"
"net/http"
)
type FHIR430Client struct {
*BaseClient
}
func NewFHIR430Client(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (*FHIR430Client, *models.Source, error) {
baseClient, updatedSource, err := NewBaseClient(ctx, appConfig, globalLogger, source, testHttpClient...)
return &FHIR430Client{
baseClient,
}, updatedSource, err
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// FHIR
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
func (c *FHIR430Client) GetPatientEverything(patientId string) (*fhir430.Bundle, error) {
// https://www.hl7.org/fhir/patient-operation-everything.html
bundle := fhir430.Bundle{}
err := c.GetRequest(fmt.Sprintf("Patient/%s/$everything", patientId), &bundle)
return &bundle, err
}
func (c *FHIR430Client) GetPatient(patientId string) (*fhir430.Patient, error) {
patient := fhir430.Patient{}
err := c.GetRequest(fmt.Sprintf("Patient/%s", patientId), &patient)
return &patient, err
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// Process Bundles
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
func (c *FHIR430Client) ProcessBundle(bundle fhir430.Bundle) ([]models.ResourceFhir, error) {
//process each entry in bundle
wrappedResourceModels := lo.FilterMap[fhir430.BundleEntry, models.ResourceFhir](bundle.Entry, func(bundleEntry fhir430.BundleEntry, _ int) (models.ResourceFhir, bool) {
originalResource, _ := fhirutils.MapToResource(bundleEntry.Resource, false)
resourceType, resourceId := originalResource.(ResourceInterface).ResourceRef()
// TODO find a way to safely/consistently get the resource updated date (and other metadata) which shoudl be added to the model.
//if originalResource.Meta != nil && originalResource.Meta.LastUpdated != nil {
// if parsed, err := time.Parse(time.RFC3339Nano, *originalResource.Meta.LastUpdated); err == nil {
// patientProfile.UpdatedAt = parsed
// }
//}
if resourceId == nil {
//no resourceId present for this resource, we'll ignore it.
return models.ResourceFhir{}, false
}
wrappedResourceModel := models.ResourceFhir{
OriginBase: models.OriginBase{
ModelBase: models.ModelBase{},
UserID: c.Source.UserID,
SourceID: c.Source.ID,
SourceResourceID: *resourceId,
SourceResourceType: resourceType,
},
Payload: datatypes.JSON(bundleEntry.Resource),
}
return wrappedResourceModel, true
})
return wrappedResourceModels, nil
}

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@ -1,19 +0,0 @@
package base
import (
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
"os"
)
//go:generate mockgen -source=interface.go -destination=mock/mock_client.go
type Client interface {
GetRequest(resourceSubpath string, decodeModelPtr interface{}) error
SyncAll(db database.DatabaseRepository) error
//Manual client ONLY functions
SyncAllBundle(db database.DatabaseRepository, bundleFile *os.File) error
}
type ResourceInterface interface {
ResourceRef() (string, *string)
}

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@ -1,116 +0,0 @@
// Code generated by MockGen. DO NOT EDIT.
// Source: interface.go
// Package mock_base is a generated GoMock package.
package mock_base
import (
os "os"
reflect "reflect"
database "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
gomock "github.com/golang/mock/gomock"
)
// MockClient is a mock of Client interface.
type MockClient struct {
ctrl *gomock.Controller
recorder *MockClientMockRecorder
}
// MockClientMockRecorder is the mock recorder for MockClient.
type MockClientMockRecorder struct {
mock *MockClient
}
// NewMockClient creates a new mock instance.
func NewMockClient(ctrl *gomock.Controller) *MockClient {
mock := &MockClient{ctrl: ctrl}
mock.recorder = &MockClientMockRecorder{mock}
return mock
}
// EXPECT returns an object that allows the caller to indicate expected use.
func (m *MockClient) EXPECT() *MockClientMockRecorder {
return m.recorder
}
// GetRequest mocks base method.
func (m *MockClient) GetRequest(resourceSubpath string, decodeModelPtr interface{}) error {
m.ctrl.T.Helper()
ret := m.ctrl.Call(m, "GetRequest", resourceSubpath, decodeModelPtr)
ret0, _ := ret[0].(error)
return ret0
}
// GetRequest indicates an expected call of GetRequest.
func (mr *MockClientMockRecorder) GetRequest(resourceSubpath, decodeModelPtr interface{}) *gomock.Call {
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "GetRequest", reflect.TypeOf((*MockClient)(nil).GetRequest), resourceSubpath, decodeModelPtr)
}
// SyncAll mocks base method.
func (m *MockClient) SyncAll(db database.DatabaseRepository) error {
m.ctrl.T.Helper()
ret := m.ctrl.Call(m, "SyncAll", db)
ret0, _ := ret[0].(error)
return ret0
}
// SyncAll indicates an expected call of SyncAll.
func (mr *MockClientMockRecorder) SyncAll(db interface{}) *gomock.Call {
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "SyncAll", reflect.TypeOf((*MockClient)(nil).SyncAll), db)
}
// SyncAllBundle mocks base method.
func (m *MockClient) SyncAllBundle(db database.DatabaseRepository, bundleFile *os.File) error {
m.ctrl.T.Helper()
ret := m.ctrl.Call(m, "SyncAllBundle", db, bundleFile)
ret0, _ := ret[0].(error)
return ret0
}
// SyncAllBundle indicates an expected call of SyncAllBundle.
func (mr *MockClientMockRecorder) SyncAllBundle(db, bundleFile interface{}) *gomock.Call {
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "SyncAllBundle", reflect.TypeOf((*MockClient)(nil).SyncAllBundle), db, bundleFile)
}
// MockResourceInterface is a mock of ResourceInterface interface.
type MockResourceInterface struct {
ctrl *gomock.Controller
recorder *MockResourceInterfaceMockRecorder
}
// MockResourceInterfaceMockRecorder is the mock recorder for MockResourceInterface.
type MockResourceInterfaceMockRecorder struct {
mock *MockResourceInterface
}
// NewMockResourceInterface creates a new mock instance.
func NewMockResourceInterface(ctrl *gomock.Controller) *MockResourceInterface {
mock := &MockResourceInterface{ctrl: ctrl}
mock.recorder = &MockResourceInterfaceMockRecorder{mock}
return mock
}
// EXPECT returns an object that allows the caller to indicate expected use.
func (m *MockResourceInterface) EXPECT() *MockResourceInterfaceMockRecorder {
return m.recorder
}
// ResourceRef mocks base method.
func (m *MockResourceInterface) ResourceRef() (string, *string) {
m.ctrl.T.Helper()
ret := m.ctrl.Call(m, "ResourceRef")
ret0, _ := ret[0].(string)
ret1, _ := ret[1].(*string)
return ret0, ret1
}
// ResourceRef indicates an expected call of ResourceRef.
func (mr *MockResourceInterfaceMockRecorder) ResourceRef() *gomock.Call {
mr.mock.ctrl.T.Helper()
return mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "ResourceRef", reflect.TypeOf((*MockResourceInterface)(nil).ResourceRef))
}

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@ -1,51 +0,0 @@
package base
import (
"context"
"crypto/tls"
"github.com/seborama/govcr"
"golang.org/x/oauth2"
"net/http"
"path"
"testing"
)
func OAuthVcrSetup(t *testing.T, enableRecording bool) *http.Client {
accessToken := "PLACEHOLDER"
if enableRecording {
//this has to be disabled because CI is empty inside docker containers.
accessToken = ""
}
ts := oauth2.StaticTokenSource(
//setting a real access token here will allow API calls to connect successfully
&oauth2.Token{AccessToken: accessToken},
)
tr := http.DefaultTransport.(*http.Transport)
tr.TLSClientConfig = &tls.Config{
InsecureSkipVerify: true, //disable certificate validation because we're playing back http requests.
}
insecureClient := http.Client{
Transport: tr,
}
ctx := context.WithValue(oauth2.NoContext, oauth2.HTTPClient, insecureClient)
tc := oauth2.NewClient(ctx, ts)
vcrConfig := govcr.VCRConfig{
Logging: true,
CassettePath: path.Join("testdata", "govcr-fixtures"),
Client: tc,
//this line ensures that we do not attempt to create new recordings.
//Comment this out if you would like to make recordings.
DisableRecording: !enableRecording,
}
// HTTP headers are case-insensitive
vcrConfig.RequestFilters.Add(govcr.RequestDeleteHeaderKeys("User-Agent", "user-agent"))
vcr := govcr.NewVCR(t.Name(), &vcrConfig)
return vcr.Client
}

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@ -1,31 +0,0 @@
package bluebutton
import (
"context"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/base"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
"github.com/sirupsen/logrus"
"net/http"
)
type BlueButtonClient struct {
*base.FHIR401Client
}
func NewClient(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (base.Client, *models.Source, error) {
baseClient, updatedSource, err := base.NewFHIR401Client(ctx, appConfig, globalLogger, source, testHttpClient...)
return BlueButtonClient{
baseClient,
}, updatedSource, err
}
func (c BlueButtonClient) SyncAll(db database.DatabaseRepository) error {
supportedResources := []string{
"ExplanationOfBenefit",
"Coverage",
}
return c.SyncAllByResourceName(db, supportedResources)
}

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@ -1,22 +0,0 @@
package careevolution
import (
"context"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/base"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
"github.com/sirupsen/logrus"
"net/http"
)
type CareEvolutionClient struct {
*base.FHIR401Client
}
func NewClient(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (base.Client, *models.Source, error) {
baseClient, updatedSource, err := base.NewFHIR401Client(ctx, appConfig, globalLogger, source, testHttpClient...)
baseClient.Headers["Accept"] = "application/json+fhir"
return CareEvolutionClient{
baseClient,
}, updatedSource, err
}

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@ -1,53 +0,0 @@
package cerner
import (
"context"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/base"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
"github.com/sirupsen/logrus"
"net/http"
)
type CernerClient struct {
*base.FHIR401Client
}
func NewClient(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (base.Client, *models.Source, error) {
baseClient, updatedSource, err := base.NewFHIR401Client(ctx, appConfig, globalLogger, source, testHttpClient...)
baseClient.Headers["Accept"] = "application/json+fhir"
return CernerClient{
baseClient,
}, updatedSource, err
}
func (c CernerClient) SyncAll(db database.DatabaseRepository) error {
supportedResources := []string{
"AllergyIntolerance",
"CarePlan",
"CareTeam",
"Condition",
"Consent",
"Device",
"Encounter",
"FamilyMemberHistory",
"Goal",
"Immunization",
"InsurancePlan",
"MedicationRequest",
"NutritionOrder",
"Observation",
"Person",
"Procedure",
"Provenance",
"Questionnaire",
"QuestionnaireResponse",
"RelatedPerson",
"Schedule",
"ServiceRequest",
"Slot",
}
return c.SyncAllByResourceName(db, supportedResources)
}

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@ -1,21 +0,0 @@
package cigna
import (
"context"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/base"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
"github.com/sirupsen/logrus"
"net/http"
)
type CignaClient struct {
*base.FHIR401Client
}
func NewClient(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (base.Client, *models.Source, error) {
baseClient, updatedSource, err := base.NewFHIR401Client(ctx, appConfig, globalLogger, source, testHttpClient...)
return CignaClient{
baseClient,
}, updatedSource, err
}

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@ -1,48 +0,0 @@
package cigna
import (
"context"
mock_config "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config/mock"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/base"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
"github.com/golang/mock/gomock"
"github.com/sirupsen/logrus"
"github.com/stretchr/testify/require"
"io/ioutil"
"os"
"testing"
)
func TestCignaClient_SyncAll(t *testing.T) {
t.Parallel()
//setup
mockCtrl := gomock.NewController(t)
defer mockCtrl.Finish()
fakeConfig := mock_config.NewMockInterface(mockCtrl)
testDatabase, err := ioutil.TempFile("testdata", "fasten.db")
require.NoError(t, err)
defer os.Remove(testDatabase.Name())
fakeConfig.EXPECT().GetString("web.database.location").AnyTimes().Return(testDatabase.Name())
testLogger := logrus.WithFields(logrus.Fields{
"type": "test",
})
httpClient := base.OAuthVcrSetup(t, false)
client, _, err := NewClient(context.Background(), fakeConfig, testLogger, models.Source{
SourceType: "cigna",
PatientId: "A00000000000005",
ApiEndpointBaseUrl: "https://p-hi2.digitaledge.cigna.com/PatientAccess/v1-devportal",
ClientId: "e434426c-2aaf-413a-a39a-8f5f6130f287",
}, httpClient)
db, err := database.NewRepository(fakeConfig, testLogger)
require.NoError(t, err)
//test
err = client.SyncAll(db)
require.NoError(t, err)
//assert
require.NoError(t, err)
}

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@ -1,54 +0,0 @@
package epic
import (
"context"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/base"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
"github.com/sirupsen/logrus"
"net/http"
)
type EpicClient struct {
*base.FHIR401Client
}
func NewClient(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (base.Client, *models.Source, error) {
baseClient, updatedSource, err := base.NewFHIR401Client(ctx, appConfig, globalLogger, source, testHttpClient...)
baseClient.Headers["Accept"] = "application/json+fhir"
return EpicClient{
baseClient,
}, updatedSource, err
}
func (c EpicClient) SyncAll(db database.DatabaseRepository) error {
supportedResources := []string{
"AllergyIntolerance",
"CarePlan",
"CareTeam",
"Condition",
"Consent",
"Device",
"Encounter",
"FamilyMemberHistory",
"Goal",
"Immunization",
"InsurancePlan",
"MedicationRequest",
"NutritionOrder",
"Observation",
"Person",
"Procedure",
"Provenance",
"Questionnaire",
"QuestionnaireResponse",
"RelatedPerson",
"Schedule",
"ServiceRequest",
"Slot",
}
return c.SyncAllByResourceName(db, supportedResources)
}

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@ -1,54 +0,0 @@
package healthit
import (
"context"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/base"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
"github.com/sirupsen/logrus"
"net/http"
)
type HealthItClient struct {
*base.FHIR401Client
}
func NewClient(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (base.Client, *models.Source, error) {
baseClient, updatedSource, err := base.NewFHIR401Client(ctx, appConfig, globalLogger, source, testHttpClient...)
baseClient.Headers["Accept"] = "application/json+fhir"
return HealthItClient{
baseClient,
}, updatedSource, err
}
func (c HealthItClient) SyncAll(db database.DatabaseRepository) error {
supportedResources := []string{
"AllergyIntolerance",
"CarePlan",
"CareTeam",
"Condition",
"Consent",
"Device",
"Encounter",
"FamilyMemberHistory",
"Goal",
"Immunization",
"InsurancePlan",
"MedicationRequest",
"NutritionOrder",
"Observation",
"Person",
"Procedure",
"Provenance",
"Questionnaire",
"QuestionnaireResponse",
"RelatedPerson",
"Schedule",
"ServiceRequest",
"Slot",
}
return c.SyncAllByResourceName(db, supportedResources)
}

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@ -1,21 +0,0 @@
package logica
import (
"context"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/base"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
"github.com/sirupsen/logrus"
"net/http"
)
type LogicaClient struct {
*base.FHIR401Client
}
func NewClient(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (base.Client, *models.Source, error) {
baseClient, updatedSource, err := base.NewFHIR401Client(ctx, appConfig, globalLogger, source, testHttpClient...)
return LogicaClient{
baseClient,
}, updatedSource, err
}

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@ -1,49 +0,0 @@
package logica
import (
"context"
mock_config "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config/mock"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/base"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
"github.com/golang/mock/gomock"
"github.com/sirupsen/logrus"
"github.com/stretchr/testify/require"
"io/ioutil"
"os"
"testing"
)
func TestLogicaClient_SyncAll(t *testing.T) {
t.Parallel()
//setup
mockCtrl := gomock.NewController(t)
defer mockCtrl.Finish()
fakeConfig := mock_config.NewMockInterface(mockCtrl)
testDatabase, err := ioutil.TempFile("", "fasten.db")
require.NoError(t, err)
defer os.Remove(testDatabase.Name())
fakeConfig.EXPECT().GetString("web.database.location").AnyTimes().Return(testDatabase.Name())
testLogger := logrus.WithFields(logrus.Fields{
"type": "test",
})
httpClient := base.OAuthVcrSetup(t, false)
client, _, err := NewClient(context.Background(), fakeConfig, testLogger, models.Source{
SourceType: "logica",
PatientId: "smart-1288992",
ApiEndpointBaseUrl: "https://api.logicahealth.org/fastenhealth/data",
ClientId: "12b14c49-a4da-42f7-9e6f-2f19db622962",
}, httpClient)
require.NoError(t, err)
db, err := database.NewRepository(fakeConfig, testLogger)
require.NoError(t, err)
//test
err = client.SyncAll(db)
require.NoError(t, err)
//assert
require.NoError(t, err)
}

File diff suppressed because one or more lines are too long

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@ -1,164 +0,0 @@
package manual
import (
"context"
"fmt"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub/internal/fhir/base"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
"github.com/fastenhealth/gofhir-models/fhir401"
fhir401utils "github.com/fastenhealth/gofhir-models/fhir401/utils"
"github.com/fastenhealth/gofhir-models/fhir430"
fhir430utils "github.com/fastenhealth/gofhir-models/fhir430/utils"
"github.com/samber/lo"
"github.com/sirupsen/logrus"
"io"
"net/http"
"os"
"strings"
)
type ManualClient struct {
Context context.Context
AppConfig config.Interface
Logger logrus.FieldLogger
Source *models.Source
}
func (m ManualClient) GetRequest(resourceSubpath string, decodeModelPtr interface{}) error {
panic("implement me")
}
func (m ManualClient) SyncAll(db database.DatabaseRepository) error {
panic("implement me")
}
func (m ManualClient) SyncAllBundle(db database.DatabaseRepository, bundleFile *os.File) error {
// we need to find the (most populated) patient record
patientId, bundleType, err := m.ExtractPatientId(bundleFile)
if err != nil {
return fmt.Errorf("an error occurred while extracting patient id from bundle: %w", err)
}
// we need to add the patient id to the source
m.Source.PatientId = patientId
// we need to upsert Source
err = db.CreateSource(m.Context, m.Source)
if err != nil {
return fmt.Errorf("an error occurred while creating manual source: %w", err)
}
// we need to parse the bundle into resources (might need to try a couple of different times)
var resourceFhirList []models.ResourceFhir
switch bundleType {
case "fhir430":
bundle430Data := fhir430.Bundle{}
err := base.ParseBundle(bundleFile, &bundle430Data)
if err != nil {
return fmt.Errorf("an error occurred while parsing 4.3.0 bundle: %w", err)
}
client, _, err := base.NewFHIR430Client(m.Context, m.AppConfig, m.Logger, *m.Source, http.DefaultClient)
if err != nil {
return fmt.Errorf("an error occurred while creating 4.3.0 client: %w", err)
}
resourceFhirList, err = client.ProcessBundle(bundle430Data)
if err != nil {
return fmt.Errorf("an error occurred while processing 4.3.0 resources: %w", err)
}
case "fhir401":
bundle401Data := fhir401.Bundle{}
err := base.ParseBundle(bundleFile, &bundle401Data)
if err != nil {
return fmt.Errorf("an error occurred while parsing 4.0.1 bundle: %w", err)
}
client, _, err := base.NewFHIR401Client(m.Context, m.AppConfig, m.Logger, *m.Source, http.DefaultClient)
if err != nil {
return fmt.Errorf("an error occurred while creating 4.0.1 client: %w", err)
}
resourceFhirList, err = client.ProcessBundle(bundle401Data)
if err != nil {
return fmt.Errorf("an error occurred while processing 4.0.1 resources: %w", err)
}
}
// we need to upsert all resources (and make sure they are associated with new Source)
for _, apiModel := range resourceFhirList {
err = db.UpsertResource(context.Background(), &apiModel)
if err != nil {
return fmt.Errorf("an error occurred while upserting resources: %w", err)
}
}
return nil
}
func (m ManualClient) ExtractPatientId(bundleFile *os.File) (string, string, error) {
// try from newest format to the oldest format
bundle430Data := fhir430.Bundle{}
bundle401Data := fhir401.Bundle{}
var patientIds []string
bundleType := "fhir430"
if err := base.ParseBundle(bundleFile, &bundle430Data); err == nil {
patientIds = lo.FilterMap[fhir430.BundleEntry, string](bundle430Data.Entry, func(bundleEntry fhir430.BundleEntry, _ int) (string, bool) {
parsedResource, err := fhir430utils.MapToResource(bundleEntry.Resource, false)
if err != nil {
return "", false
}
typedResource := parsedResource.(base.ResourceInterface)
resourceType, resourceId := typedResource.ResourceRef()
if resourceId == nil || len(*resourceId) == 0 {
return "", false
}
return *resourceId, resourceType == fhir430.ResourceTypePatient.String()
})
}
bundleFile.Seek(0, io.SeekStart)
//fallback
if patientIds == nil || len(patientIds) == 0 {
bundleType = "fhir401"
//try parsing the bundle as a 401 bundle
//TODO: find a better, more generic way to do this.
err := base.ParseBundle(bundleFile, &bundle401Data)
if err != nil {
return "", "", err
}
patientIds = lo.FilterMap[fhir401.BundleEntry, string](bundle401Data.Entry, func(bundleEntry fhir401.BundleEntry, _ int) (string, bool) {
parsedResource, err := fhir401utils.MapToResource(bundleEntry.Resource, false)
if err != nil {
return "", false
}
typedResource := parsedResource.(base.ResourceInterface)
resourceType, resourceId := typedResource.ResourceRef()
if resourceId == nil || len(*resourceId) == 0 {
return "", false
}
return *resourceId, resourceType == fhir430.ResourceTypePatient.String()
})
}
bundleFile.Seek(0, io.SeekStart)
if patientIds == nil || len(patientIds) == 0 {
return "", "", fmt.Errorf("could not determine patient id")
} else {
//reset reader
return strings.TrimLeft(patientIds[0], "Patient/"), bundleType, nil
}
}
func NewClient(ctx context.Context, appConfig config.Interface, globalLogger logrus.FieldLogger, source models.Source, testHttpClient ...*http.Client) (base.Client, *models.Source, error) {
return ManualClient{
Context: ctx,
AppConfig: appConfig,
Logger: globalLogger,
Source: &models.Source{
SourceType: pkg.SourceTypeManual,
},
}, nil, nil
}

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@ -1,50 +0,0 @@
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 *Source `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
}

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

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@ -1,49 +0,0 @@
package models
import (
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg"
"github.com/google/uuid"
)
// Source Data/Medical Provider Credentials
type Source 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"`
PatientId string `json:"patient_id" gorm:"uniqueIndex:idx_user_source_patient"`
//oauth endpoints
OauthAuthorizationEndpoint string `json:"oauth_authorization_endpoint"`
OauthTokenEndpoint string `json:"oauth_token_endpoint"`
OauthRegistrationEndpoint string `json:"oauth_registration_endpoint"`
OauthIntrospectionEndpoint string `json:"oauth_introspection_endpoint"`
OauthUserInfoEndpoint string `json:"oauth_userinfo_endpoint"`
OauthTokenEndpointAuthMethods string `json:"oauth_token_endpoint_auth_methods_supported"`
ApiEndpointBaseUrl string `json:"api_endpoint_base_url"`
ClientId string `json:"client_id"`
RedirectUri string `json:"redirect_uri"`
Scopes string `json:"scopes"`
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"`
Confidential bool `json:"confidential"`
}
/*
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
*/

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

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

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@ -1,26 +1,6 @@
package models
import "golang.org/x/crypto/bcrypt"
type User struct {
ModelBase
Name string `json:"name"`
Username string `json:"username" gorm:"unique"`
Username string `json:"username"`
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
}

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@ -1,9 +1,6 @@
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"
@ -12,57 +9,17 @@ import (
func AuthSignup(c *gin.Context) {
databaseRepo := c.MustGet("REPOSITORY").(database.DatabaseRepository)
appConfig := c.MustGet("CONFIG").(config.Interface)
var user models.User
if err := c.ShouldBindJSON(&user); err != nil {
c.JSON(http.StatusInternalServerError, gin.H{"success": false})
c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": err.Error()})
return
}
err := databaseRepo.CreateUser(c, &user)
if err != nil {
c.JSON(http.StatusInternalServerError, gin.H{"success": false})
c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": err.Error()})
return
}
// return JWT
tokenString, err := auth.GenerateJWT(appConfig.GetString("web.jwt.encryptionkey"), user.Username, user.ID.String())
if err != nil {
c.JSON(http.StatusInternalServerError, gin.H{"success": false})
return
}
c.JSON(http.StatusOK, gin.H{"success": true, "data": tokenString})
}
func AuthSignin(c *gin.Context) {
databaseRepo := c.MustGet("REPOSITORY").(database.DatabaseRepository)
appConfig := c.MustGet("CONFIG").(config.Interface)
var user models.User
if err := c.ShouldBindJSON(&user); err != nil {
c.JSON(http.StatusInternalServerError, gin.H{"success": false})
return
}
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.StatusUnauthorized, gin.H{"success": false, "error": fmt.Sprintf("username or password does not match: %s", user.Username)})
return
}
// return JWT
tokenString, err := auth.GenerateJWT(appConfig.GetString("web.jwt.encryptionkey"), user.Username, user.ID.String())
if err != nil {
c.JSON(http.StatusInternalServerError, gin.H{"success": false, "error": "an error occurred generating JWT token"})
return
}
c.JSON(http.StatusOK, gin.H{"success": true, "data": tokenString})
c.JSON(http.StatusOK, gin.H{"success": true})
}

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@ -0,0 +1,52 @@
package handler
import (
"fmt"
"github.com/gin-gonic/gin"
"log"
"net/http"
"net/http/httputil"
"net/url"
"strings"
)
//TODO, there are security implications to this, we need to make sure we lock this down.
func CORSProxy(c *gin.Context) {
//appConfig := c.MustGet("CONFIG").(config.Interface)
corsUrl := fmt.Sprintf("https://%s", strings.TrimPrefix(c.Param("proxyPath"), "/"))
remote, err := url.Parse(corsUrl)
remote.RawQuery = c.Request.URL.Query().Encode()
if err != nil {
panic(err)
}
proxy := httputil.ReverseProxy{}
//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 = remote.Path
//TODO: throw an error if the remote.Host is not allowed
}
proxy.ModifyResponse = func(r *http.Response) error {
//b, _ := ioutil.ReadAll(r.Body)
//buf := bytes.NewBufferString("Monkey")
//buf.Write(b)
//r.Body = ioutil.NopCloser(buf)
r.Header.Set("Access-Control-Allow-Methods", "GET,HEAD")
r.Header.Set("Access-Control-Allow-Credentials", "true")
r.Header.Set("Access-Control-Allow-Origin", "*")
return nil
}
proxy.ServeHTTP(c.Writer, c.Request)
}

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@ -0,0 +1,40 @@
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("web.couchdb.scheme"), appConfig.GetString("web.couchdb.host"), appConfig.GetString("web.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)
}

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@ -1,35 +0,0 @@
package handler
import (
//"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
"github.com/gin-gonic/gin"
//"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/config"
//"github.com/sirupsen/logrus"
"net/http"
)
func GetHelloWorld(c *gin.Context) {
//logger := c.MustGet("LOGGER").(*logrus.Entry)
//appConfig := c.MustGet("CONFIG").(config.Interface)
//device, err := deviceRepo.GetDeviceDetails(c, c.Param("wwn"))
//if err != nil {
// logger.Errorln("An error occurred while retrieving device details", err)
// c.JSON(http.StatusInternalServerError, gin.H{"success": false})
// return
//}
//
//durationKey, exists := c.GetQuery("duration_key")
//if !exists {
// durationKey = "forever"
//}
//
//smartResults, err := deviceRepo.GetSmartAttributeHistory(c, c.Param("wwn"), durationKey, nil)
//if err != nil {
// logger.Errorln("An error occurred while retrieving device smart results", err)
// c.JSON(http.StatusInternalServerError, gin.H{"success": false})
// return
//}
c.JSON(http.StatusOK, gin.H{"success": true, "data": map[string]interface{}{"hello": "world"}})
}

View File

@ -1,51 +0,0 @@
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})
}

View File

@ -1,232 +0,0 @@
package handler
import (
"fmt"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/database"
"github.com/fastenhealth/fastenhealth-onprem/backend/pkg/hub"
"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.Source{}
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 Source 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
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, "data": sourceCred})
}
func SourceSync(c *gin.Context) {
logger := c.MustGet("LOGGER").(*logrus.Entry)
databaseRepo := c.MustGet("REPOSITORY").(database.DatabaseRepository)
logger.Infof("Get Source 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
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, "data": sourceCred})
}
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 "Source" object yet, as we do not know the patientID
// create a "manual" client, which we can use to parse the
manualSourceClient, _, err := hub.NewClient(pkg.SourceTypeManual, c, nil, logger, models.Source{})
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
}
err = manualSourceClient.SyncAllBundle(databaseRepo, bundleFile)
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": fmt.Sprintf("'%s' uploaded!", file.Filename)})
}
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 := hub.NewClient(foundSource.SourceType, c, nil, 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
}
if updatedSource != nil {
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.Source) error {
// after creating the source, we should do a bulk import
sourceClient, updatedSource, err := hub.NewClient(sourceCred.SourceType, c, nil, logger, sourceCred)
if err != nil {
logger.Errorln("An error occurred while initializing hub client using source credential", err)
return err
}
if updatedSource != nil {
err := databaseRepo.CreateSource(c, updatedSource)
if err != nil {
logger.Errorln("An error occurred while updating source credential", err)
return err
}
}
err = sourceClient.SyncAll(databaseRepo)
if err != nil {
logger.Errorln("An error occurred while bulk import of resources from source", err)
return err
}
return nil
}

View File

@ -1,21 +0,0 @@
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})
}

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@ -1,47 +0,0 @@
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.ValidateToken(appConfig.GetString("web.jwt.encryptionkey"), 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.Username)
c.Set("AUTH_USERID", claim.UserId)
c.Next()
}
}

View File

@ -41,31 +41,11 @@ func (ae *AppEngine) Setup(logger *logrus.Entry) *gin.Engine {
})
api.POST("/auth/signup", handler.AuthSignup)
api.POST("/auth/signin", handler.AuthSignin)
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)
}
api.GET("/metadata/source", handler.GetMetadataSource)
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)
}
r.Any("/database/*proxyPath", handler.CouchDBProxy)
r.GET("/cors/*proxyPath", handler.CORSProxy)
r.OPTIONS("/cors/*proxyPath", handler.CORSProxy)
}
}

View File

@ -6,9 +6,6 @@
version: 1
web:
jwt:
# used to encrypt/validate JWT session key (used for authentication)
encryptionkey: 'changethissupersecretkey'
listen:
port: 8080
host: 0.0.0.0

16
docker-compose.yml Normal file
View File

@ -0,0 +1,16 @@
version: "3.9"
services:
couchdb:
build:
context: .
dockerfile: Dockerfile
# environment:
# - COUCHDB_USER=admin
# - COUCHDB_PASSWORD=password
ports:
- "9090:8080"
- "5984:5984"
volumes:
- ./.couchdb/data:/opt/couchdb/data
- ./.couchdb/config:/opt/couchdb/etc/local.d
# - ./config.example.yaml:/opt/fasten/config/config.yaml

9
docker/README.md Normal file
View File

@ -0,0 +1,9 @@
# Dockerfiles
Note, the context for Dockerfiles in this directory is **always** the repository root.
```bash
docker build -f docker/couchdb/Dockerfile -t couchdb-fasten .
docker run --rm -it -p 5984:5984 -v `pwd`/.couchdb/data:/opt/couchdb/data -v `pwd`/.couchdb/config:/opt/couchdb/etc/local.d couchdb-fasten
```

16
docker/couchdb/Dockerfile Normal file
View File

@ -0,0 +1,16 @@
#########################################################################################################
# CouchDB Build
# NOTE: the context for this build should be the root of the repository.
#########################################################################################################
FROM couchdb:3.2
ARG S6_ARCH=amd64
RUN curl https://github.com/just-containers/s6-overlay/releases/download/v1.21.8.0/s6-overlay-${S6_ARCH}.tar.gz -L -s --output /tmp/s6-overlay-${S6_ARCH}.tar.gz \
&& tar xzf /tmp/s6-overlay-${S6_ARCH}.tar.gz -C / \
&& rm -rf /tmp/s6-overlay-${S6_ARCH}.tar.gz
COPY /docker/couchdb/local.ini /opt/couchdb/etc/local.ini
COPY /docker/rootfs /
RUN rm -rf /etc/services.d/fasten #delete the fasten app from the couchdbase container.
ENTRYPOINT ["/init"]

108
docker/couchdb/local.ini Normal file
View File

@ -0,0 +1,108 @@
; CouchDB Configuration Settings
; Custom settings should be made in this file. They will override settings
; in default.ini, but unlike changes made to default.ini, this file won't be
; overwritten on server upgrade.
[cors]
origins = *
headers = accept, authorization, content-type, origin, referer
credentials = true
methods = GET, PUT, POST, HEAD, DELETE
[couchdb]
;max_document_size = 4294967296 ; bytes
;os_process_timeout = 5000
single_node=true
[couch_peruser]
; If enabled, couch_peruser ensures that a private per-user database
; exists for each document in _users. These databases are writable only
; by the corresponding user. Databases are in the following form:
; userdb-{hex encoded username}
enable = true
; If set to true and a user is deleted, the respective database gets
; deleted as well.
;delete_dbs = true
; Set a default q value for peruser-created databases that is different from
; cluster / q
;q = 1
[chttpd]
;port = 5984
;bind_address = 127.0.0.1
; Options for the MochiWeb HTTP server.
;server_options = [{backlog, 128}, {acceptor_pool_size, 16}]
; For more socket options, consult Erlang's module 'inet' man page.
;socket_options = [{sndbuf, 262144}, {nodelay, true}]
bind_address = 0.0.0.0
enable_cors = true
x_forwarded_host = X-Forwarded-Host
[httpd]
; NOTE that this only configures the "backend" node-local port, not the
; "frontend" clustered port. You probably don't want to change anything in
; this section.
; Uncomment next line to trigger basic-auth popup on unauthorized requests.
;WWW-Authenticate = Basic realm="administrator"
; Uncomment next line to set the configuration modification whitelist. Only
; whitelisted values may be changed via the /_config URLs. To allow the admin
; to change this value over HTTP, remember to include {httpd,config_whitelist}
; itself. Excluding it from the list would require editing this file to update
; the whitelist.
;config_whitelist = [{httpd,config_whitelist}, {log,level}, {etc,etc}]
enable_cors = true
[chttpd_auth]
; If you set this to true, you should also uncomment the WWW-Authenticate line
; above. If you don't configure a WWW-Authenticate header, CouchDB will send
; Basic realm="server" in order to prevent you getting logged out.
; require_valid_user = false
allow_persistent_cookies = true
;cookie_domain = localhost:5984
[ssl]
;enable = true
;cert_file = /full/path/to/server_cert.pem
;key_file = /full/path/to/server_key.pem
;password = somepassword
; set to true to validate peer certificates
;verify_ssl_certificates = false
; Set to true to fail if the client does not send a certificate. Only used if verify_ssl_certificates is true.
;fail_if_no_peer_cert = false
; Path to file containing PEM encoded CA certificates (trusted
; certificates used for verifying a peer certificate). May be omitted if
; you do not want to verify the peer.
;cacert_file = /full/path/to/cacertf
; The verification fun (optional) if not specified, the default
; verification fun will be used.
;verify_fun = {Module, VerifyFun}
; maximum peer certificate depth
;ssl_certificate_max_depth = 1
;
; Reject renegotiations that do not live up to RFC 5746.
;secure_renegotiate = true
; The cipher suites that should be supported.
; Can be specified in erlang format "{ecdhe_ecdsa,aes_128_cbc,sha256}"
; or in OpenSSL format "ECDHE-ECDSA-AES128-SHA256".
;ciphers = ["ECDHE-ECDSA-AES128-SHA256", "ECDHE-ECDSA-AES128-SHA"]
; The SSL/TLS versions to support
;tls_versions = [tlsv1, 'tlsv1.1', 'tlsv1.2']
; To enable Virtual Hosts in CouchDB, add a vhost = path directive. All requests to
; the Virual Host will be redirected to the path. In the example below all requests
; to http://example.com/ are redirected to /database.
; If you run CouchDB on a specific port, include the port number in the vhost:
; example.com:5984 = /database
[vhosts]
;example.com = /database/
; To create an admin account uncomment the '[admins]' section below and add a
; line in the format 'username = password'. When you next start CouchDB, it
; will change the password to a hash (so that your passwords don't linger
; around in plain-text files). You can add more admin accounts with more
; 'username = password' lines. Don't forget to restart CouchDB after
; changing this.
[admins]
admin = mysecretpassword

View File

@ -0,0 +1,7 @@
#!/usr/bin/with-contenv bash
if [ -n "${TZ}" ]
then
ln -snf "/usr/share/zoneinfo/${TZ}" /etc/localtime
echo "${TZ}" > /etc/timezone
fi

View File

@ -0,0 +1,35 @@
#!/usr/bin/with-contenv bash
if [ -f "/opt/couchdb/data/.init_complete" ]; then
echo "Couchdb initialization has already completed, skipping"
else
# start couchdb as a background process (store PID)
echo "Couchdb initialization: start couchdb in background mode (non-standard port)"
# https://linux.die.net/man/1/couchdb
sed -i -e 's/;port = 5984/port = 5432/g' /opt/couchdb/etc/local.ini
sed -i -e 's/bind_address = 0.0.0.0/bind_address = 127.0.0.1/g' /opt/couchdb/etc/local.ini
/opt/couchdb/bin/couchdb -b &
COUCHDB_PID=$!
# wait for couchdb to be ready
until $(curl --output /dev/null --silent --head --fail http://127.0.0.1:5432/_up); do echo "couchdb not ready" && sleep 5; done
# create couch_peruser required system databases manually on startup
echo "couchdb ready, start creating system databases"
curl --fail -X PUT -u admin:mysecretpassword http://127.0.0.1:5432/_users
curl --fail -X PUT -u admin:mysecretpassword http://127.0.0.1:5432/_replicator
curl --fail -X PUT -u admin:mysecretpassword http://127.0.0.1:5432/_global_changes
echo "system databases created successfully"
# gracefully stop couchdb process
echo "killing couchdb process"
/opt/couchdb/bin/couchdb -k
sed -i -e 's/port = 5432/;port = 5984/g' /opt/couchdb/etc/local.ini
sed -i -e 's/bind_address = 127.0.0.1/bind_address = 0.0.0.0/g' /opt/couchdb/etc/local.ini
# create the init complete flag
echo "Couchdb initialization: complete"
touch /opt/couchdb/data/.init_complete
fi

View File

@ -0,0 +1,4 @@
#!/usr/bin/with-contenv bash
echo "starting couchdb"
/docker-entrypoint.sh /opt/couchdb/bin/couchdb

View File

@ -0,0 +1,7 @@
#!/usr/bin/with-contenv bash
# wait for couchdb to be ready
until $(curl --output /dev/null --silent --head --fail http://127.0.0.1:5984/_up); do echo "couchdb not ready" && sleep 5; done
echo "starting fasten"
/opt/fasten/fasten start --config /opt/fasten/config/config.yaml

View File

@ -34,7 +34,8 @@
],
"scripts": [
"node_modules/@panva/oauth4webapi/build/index.js"
]
],
"webWorkerTsConfig": "tsconfig.worker.json"
},
"configurations": {
"production": {
@ -125,7 +126,8 @@
"styles": [
"src/styles.scss"
],
"scripts": []
"scripts": [],
"webWorkerTsConfig": "tsconfig.worker.json"
}
},
"lint": {

View File

@ -31,14 +31,22 @@
"@swimlane/ngx-datatable": "^20.0.0",
"bootstrap": "^4.4.1",
"chart.js": "2.9.4",
"crypto-pouch": "^4.0.1",
"fhirclient": "^2.5.1",
"humanize-duration": "^3.27.3",
"moment": "^2.29.4",
"ng2-charts": "^2.3.0",
"ngx-dropzone": "^3.1.0",
"ngx-highlightjs": "^7.0.1",
"ngx-moment": "^6.0.2",
"observable-webworker": "^4.0.1",
"pouchdb": "^7.3.0",
"pouchdb-authentication": "^1.1.3",
"pouchdb-find": "^7.3.0",
"pouchdb-upsert": "^2.2.0",
"rxjs": "~6.5.4",
"tslib": "^2.0.0",
"uuid": "^9.0.0",
"zone.js": "~0.11.8"
},
"devDependencies": {
@ -46,9 +54,11 @@
"@angular/cli": "^14.1.3",
"@angular/compiler-cli": "^14.1.3",
"@angular/language-service": "^14.1.3",
"@types/crypto-pouch": "^4.0.1",
"@types/jasmine": "~3.5.0",
"@types/jasminewd2": "~2.0.3",
"@types/node": "^12.11.1",
"@types/pouchdb": "^6.4.0",
"@types/pouchdb-find": "^7.3.0",
"codelyzer": "^5.1.2",
"jasmine-core": "~3.5.0",
"jasmine-spec-reporter": "~5.0.0",

View File

@ -18,7 +18,7 @@ const routes: Routes = [
{ path: '', redirectTo: '/dashboard', pathMatch: 'full' },
{ path: 'dashboard', component: DashboardComponent, canActivate: [ CanActivateAuthGuard] },
{ path: 'source/:source_id', component: SourceDetailComponent, canActivate: [ CanActivateAuthGuard] },
{ path: 'source/:source_id/resource/:resource_id', component: ResourceDetailComponent, canActivate: [ CanActivateAuthGuard] },
{ path: 'resource/:resource_id', component: ResourceDetailComponent, canActivate: [ CanActivateAuthGuard] },
{ path: 'sources', component: MedicalSourcesComponent, canActivate: [ CanActivateAuthGuard] },
{ path: 'sources/callback/:source_type', component: MedicalSourcesComponent, canActivate: [ CanActivateAuthGuard] },

View File

@ -1,5 +1,6 @@
<div>
<app-header *ngIf="showHeader"></app-header>
<app-toast aria-live="polite" aria-atomic="true"></app-toast>
<div class="az-content-wrapper">
<router-outlet></router-outlet>
</div>

View File

@ -1,5 +1,9 @@
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({
selector: 'app-root',
@ -13,7 +17,7 @@ export class AppComponent implements OnInit {
showHeader:boolean = false;
showFooter:boolean = true;
constructor(private router: Router) {}
constructor(private router: Router, private queueService: QueueService, private toastService: ToastService) {}
ngOnInit() {

View File

@ -18,13 +18,13 @@ import { AuthSignupComponent } from './pages/auth-signup/auth-signup.component';
import { AuthSigninComponent } from './pages/auth-signin/auth-signin.component';
import { FormsModule } from '@angular/forms';
import { NgxDropzoneModule } from 'ngx-dropzone';
import { AuthInterceptorService } from './services/auth-interceptor.service';
import { CanActivateAuthGuard } from './services/can-activate.auth-guard';
import {FastenApiService} from './services/fasten-api.service';
import {FastenDbService} from './services/fasten-db.service';
import {Router} from '@angular/router';
import { SourceDetailComponent } from './pages/source-detail/source-detail.component';
import {ResourceListComponent} from './components/resource-list/resource-list.component';
import { HighlightModule, HIGHLIGHT_OPTIONS } from 'ngx-highlightjs';
import {AuthInterceptorService} from './services/auth-interceptor.service';
import { MomentModule } from 'ngx-moment';
@NgModule({
declarations: [
@ -48,14 +48,15 @@ import { HighlightModule, HIGHLIGHT_OPTIONS } from 'ngx-highlightjs';
NgbModule,
ChartsModule,
NgxDropzoneModule,
HighlightModule
HighlightModule,
MomentModule
],
providers: [
{
provide: HTTP_INTERCEPTORS,
useClass: AuthInterceptorService,
multi: true,
deps: [FastenApiService, Router]
deps: [FastenDbService, Router]
},
CanActivateAuthGuard,
{

View File

@ -1,5 +1,5 @@
import { Component, OnInit } from '@angular/core';
import {FastenApiService} from '../../services/fasten-api.service';
import {FastenDbService} from '../../services/fasten-db.service';
import { Router } from '@angular/router';
@Component({
selector: 'app-header',
@ -8,7 +8,7 @@ import { Router } from '@angular/router';
})
export class HeaderComponent implements OnInit {
constructor(private fastenApi: FastenApiService, private router: Router) { }
constructor(private fastenDb: FastenDbService, private router: Router) { }
ngOnInit() {
}
@ -24,7 +24,7 @@ export class HeaderComponent implements OnInit {
}
signOut(e) {
this.fastenApi.logout()
this.router.navigate(['auth/signin']);
this.fastenDb.Logout()
.then(() => this.router.navigate(['auth/signin']))
}
}

View File

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

View File

@ -1,7 +1,8 @@
import {ChangeDetectorRef, Component, Input, OnInit} from '@angular/core';
import {ResourceFhir} from '../../models/fasten/resource_fhir';
import {ResourceFhir} from '../../../lib/models/database/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',
@ -21,4 +22,5 @@ export class ListFallbackResourceComponent implements OnInit, ResourceListCompo
markForCheck(){
this.changeRef.markForCheck()
}
}

View File

@ -1,9 +1,9 @@
import {ChangeDetectorRef, Component, Input, OnChanges, OnInit, SimpleChanges, ViewChild} from '@angular/core';
import {ChangeDetectorRef, Component, Input, OnInit, ViewChild} from '@angular/core';
import {DatatableComponent, ColumnMode, SelectionType} from '@swimlane/ngx-datatable';
import {ResourceFhir} from '../../models/fasten/resource_fhir';
import {ResourceFhir} from '../../../lib/models/database/resource_fhir';
import {FORMATTERS, getPath, obsValue, attributeXTime} from './utils';
import {observableToBeFn} from 'rxjs/internal/testing/TestScheduler';
import {Router} from '@angular/router';
import {Base64} from '../../../lib/utils/base64';
//all Resource list components must implement this Interface
export interface ResourceListComponentInterface {
@ -61,6 +61,7 @@ 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
@ -68,7 +69,7 @@ export class ListGenericResourceComponent implements OnInit, ResourceListCompone
this.columnDefinitions.forEach((defn) => {
try{
let resourceProp = defn.getter(resource.payload)
let resourceProp = defn.getter(resource.resource_raw)
let resourceFormatted = defn.format ? FORMATTERS[defn.format](resourceProp) : resourceProp
row[defn.title.replace(/[^A-Z0-9]/ig, "_")] = resourceFormatted
}catch (e){
@ -79,9 +80,14 @@ export class ListGenericResourceComponent implements OnInit, ResourceListCompone
})
}
/**
* The selected object is NOT a ResourceFHIR, its actually a dynamically created row object
* created in renderList()
* @param selected
*/
onSelect({ selected }) {
console.log('Select Event', selected);
this.router.navigateByUrl(`/source/${selected[0].source_id}/resource/${selected[0].source_resource_id}`);
this.router.navigateByUrl(`/resource/${Base64.Encode(selected[0]._id)}`);
}
}

View File

@ -1,8 +1,8 @@
import { ResourceListOutletDirective } from './resource-list-outlet.directive';
describe('ResourceListOutletDirective', () => {
it('should create an instance', () => {
const directive = new ResourceListOutletDirective();
expect(directive).toBeTruthy();
});
});
// describe('ResourceListOutletDirective', () => {
// it('should create an instance', () => {
// const directive = new ResourceListOutletDirective();
// expect(directive).toBeTruthy();
// });
// });

View File

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

View File

@ -32,6 +32,8 @@ import {ListDiagnosticReportComponent} from './list-generic-resource/list-diagno
import {ListGoalComponent} from './list-generic-resource/list-goal.component';
import { ListFallbackResourceComponent } from './list-fallback-resource/list-fallback-resource.component';
import {NgbModule} from '@ng-bootstrap/ng-bootstrap';
import { ToastComponent } from './toast/toast.component';
import { MomentModule } from 'ngx-moment';
@NgModule({
imports: [
@ -39,6 +41,7 @@ import {NgbModule} from '@ng-bootstrap/ng-bootstrap';
BrowserModule,
NgxDatatableModule,
NgbModule,
MomentModule,
],
declarations: [
ComponentsSidebarComponent,
@ -70,6 +73,7 @@ import {NgbModule} from '@ng-bootstrap/ng-bootstrap';
ResourceListComponent,
ResourceListOutletDirective,
ListFallbackResourceComponent,
ToastComponent,
],
exports: [
ComponentsSidebarComponent,
@ -99,7 +103,8 @@ import {NgbModule} from '@ng-bootstrap/ng-bootstrap';
ListDiagnosticReportComponent,
ListGoalComponent,
ResourceListComponent,
ResourceListOutletDirective
ResourceListOutletDirective,
ToastComponent,
]
})

View File

@ -0,0 +1,17 @@
<div class="toast-container">
<ngb-toast
*ngFor="let toast of toastService.toasts"
[class]="toast.displayClass"
[autohide]="toast.autohide"
[delay]="toast.delay || 5000"
(hidden)="toastService.remove(toast)"
>
<ng-template ngbToastHeader>
<h6 class="tx-inverse tx-14 mg-b-0 mg-r-auto">{{toast.title}}</h6>
<small>{{toast.event_date | amTimeAgo}}</small>
</ng-template>
{{ toast.message }}
</ngb-toast>
</div>

View File

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

View File

@ -0,0 +1,15 @@
import {Component, OnInit, TemplateRef} from '@angular/core';
import {ToastService} from '../../services/toast.service';
@Component({
selector: 'app-toast',
templateUrl: './toast.component.html',
styleUrls: ['./toast.component.scss']
})
export class ToastComponent implements OnInit {
constructor(public toastService: ToastService) {}
ngOnInit(): void {
}
}

View File

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

View File

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

View File

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

View File

@ -0,0 +1,14 @@
export enum ToastType {
Error = "error",
Success = "success",
Info = "info"
}
export class ToastNotification {
event_date: Date = new Date()
title?: string
message: string
type: ToastType = ToastType.Info
displayClass: string = 'demo-static-toast'
autohide: boolean = true
}

View File

@ -0,0 +1,9 @@
import {Source} from '../../../lib/models/database/source';
export class SourceSyncMessage {
source: Source
userIdentifier: string
encryptionKey?: string
response?: any
}

View File

@ -7,18 +7,15 @@
<form (ngSubmit)="signinSubmit()" #userForm="ngForm">
<div class="form-group">
<label>Email</label>
<input [(ngModel)]="existingUser.username" name="username" #username="ngModel" required minlength="2" type="text" class="form-control" placeholder="Enter your email">
<label>Username</label>
<input [(ngModel)]="existingUser.username" name="username" #username="ngModel" required minlength="2" type="text" class="form-control" placeholder="Enter your username">
<div *ngIf="username.invalid && (username.dirty || username.touched)" class="alert alert-danger">
<div *ngIf="username.errors?.['required']">
Email is required.
Username is required.
</div>
<div *ngIf="username.errors?.['minlength']">
Email must be at least 4 characters long.
</div>
<div *ngIf="username.errors?.['email']">
Email is not a valid email address.
Username must be at least 4 characters long.
</div>
</div>
</div><!-- form-group -->

View File

@ -1,7 +1,9 @@
import { Component, OnInit } from '@angular/core';
import {User} from '../../models/fasten/user';
import {FastenApiService} from '../../services/fasten-api.service';
import {Component, OnInit} from '@angular/core';
import {User} from '../../../lib/models/fasten/user';
import {FastenDbService} from '../../services/fasten-db.service';
import {Router} from '@angular/router';
import {ToastService} from '../../services/toast.service';
import {ToastNotification, ToastType} from '../../models/fasten/toast';
@Component({
selector: 'app-auth-signin',
@ -13,7 +15,7 @@ export class AuthSigninComponent implements OnInit {
existingUser: User = new User()
errorMsg: string = ""
constructor(private fastenApi: FastenApiService, private router: Router) { }
constructor(private fastenDb: FastenDbService, private router: Router, private toastService: ToastService) { }
ngOnInit(): void {
}
@ -21,11 +23,19 @@ export class AuthSigninComponent implements OnInit {
signinSubmit(){
this.submitted = true;
this.fastenApi.signin(this.existingUser.username, this.existingUser.password).subscribe((tokenResp: any) => {
console.log(tokenResp);
this.router.navigateByUrl('/dashboard');
}, (err)=>{
this.errorMsg = err?.error?.error || "an unknown error occurred during sign-in"
})
this.fastenDb.Signin(this.existingUser.username, this.existingUser.password)
.then(() => this.router.navigateByUrl('/dashboard'))
.catch((err)=>{
if(err?.name){
this.errorMsg = "username or password is incorrect"
} else{
this.errorMsg = "an unknown error occurred during sign-in"
}
const toastNotificaiton = new ToastNotification()
toastNotificaiton.type = ToastType.Error
toastNotificaiton.message = this.errorMsg
this.toastService.show(toastNotificaiton)
})
}
}

View File

@ -19,33 +19,17 @@
<h4>Create an account, and get started.</h4>
<form (ngSubmit)="signupSubmit()" #userForm="ngForm">
<div class="form-group">
<label>Firstname &amp; Lastname</label>
<input [(ngModel)]="newUser.name" name="name" #name="ngModel" required minlength="2" type="text" class="form-control" placeholder="Enter your firstname and lastname">
<div *ngIf="name.invalid && (name.dirty || name.touched)" class="alert alert-danger">
<div *ngIf="name.errors?.['required']">
Name is required.
</div>
<div *ngIf="name.errors?.['minlength']">
Name must be at least 4 characters long.
</div>
</div>
</div><!-- form-group -->
<div class="form-group">
<label>Email</label>
<input [(ngModel)]="newUser.username" name="username" #username="ngModel" required email="true" minlength="5" type="text" class="form-control" placeholder="Enter your email">
<label>Username</label>
<input [(ngModel)]="newUser.username" name="username" #username="ngModel" required minlength="5" type="text" class="form-control" placeholder="Enter your username">
<div *ngIf="username.invalid && (username.dirty || username.touched)" class="alert alert-danger">
<div *ngIf="username.errors?.['required']">
Email is required.
Username is required.
</div>
<div *ngIf="username.errors?.['minlength']">
Email must be at least 4 characters long.
</div>
<div *ngIf="username.errors?.['email']">
Email is not a valid email address.
Username must be at least 4 characters long.
</div>
</div>

View File

@ -1,7 +1,9 @@
import { Component, OnInit } from '@angular/core';
import {FastenApiService} from '../../services/fasten-api.service';
import {User} from '../../models/fasten/user';
import {FastenDbService} from '../../services/fasten-db.service';
import {User} from '../../../lib/models/fasten/user';
import {Router} from '@angular/router';
import {ToastNotification, ToastType} from '../../models/fasten/toast';
import {ToastService} from '../../services/toast.service';
@Component({
selector: 'app-auth-signup',
@ -13,7 +15,12 @@ export class AuthSignupComponent implements OnInit {
newUser: User = new User()
errorMsg: string = ""
constructor(private fastenApi: FastenApiService, private router: Router) { }
constructor(
// private fastenApi: FastenApiService,
private fastenDb: FastenDbService,
private router: Router,
private toastService: ToastService
) { }
ngOnInit(): void {
}
@ -21,13 +28,26 @@ export class AuthSignupComponent implements OnInit {
signupSubmit(){
this.submitted = true;
this.fastenApi.signup(this.newUser).subscribe((tokenResp: any) => {
this.fastenDb.Signup(this.newUser).then((tokenResp: any) => {
console.log(tokenResp);
this.router.navigateByUrl('/dashboard');
},
(err)=>{
this.errorMsg = err?.error?.error || "an unknown error occurred during sign-up"
console.error("an error occured while signup",err)
if(err.name === 'conflict') {
// "batman" already exists, choose another username
this.errorMsg = "username already exists"
} else if (err.name === 'forbidden') {
// invalid username
this.errorMsg = "invalid username"
} else {
this.errorMsg = "an unknown error occurred during sign-up"
}
const toastNotificaiton = new ToastNotification()
toastNotificaiton.type = ToastType.Error
toastNotificaiton.message = this.errorMsg
this.toastService.show(toastNotificaiton)
})
}

View File

@ -148,15 +148,15 @@
<div class="media-body">
<h5>{{metadataSource[source.source_type]?.display}}</h5>
<p>
{{getPatientSummary(patientForSource[source.id]?.payload)}}
{{getPatientSummary(patientForSource[source._id]?.resource_raw)}}
</p>
</div>
</div>
</td>
<td class="align-middle"><p><small class="tx-gray-600">status:</small><br/> {{isActive(source)}}</p></td>
<td class="align-middle"><p><small class="tx-gray-600">last updated:</small><br/> {{source.updated_at | date}}</p></td>
<td class="align-middle"><p><small class="tx-gray-600">expires:</small><br/> {{source.expires_at}}</p></td>
<td class="align-middle"><p><small class="tx-gray-600">last updated:</small><br/> <span [ngbTooltip]="source.updated_at | date">{{source.updated_at | amTimeAgo}}</span></p></td>
<td class="align-middle"><p><small class="tx-gray-600">expires:</small><br/> <span [ngbTooltip]="source.expires_at | amFromUnix | date">{{source.expires_at | amFromUnix | amTimeAgo}}</span></p></td>
<td class="align-middle"><p><i class="fas fa-chevron-right"></i></td>
</tr>

View File

@ -1,12 +1,13 @@
import { Component, OnInit } from '@angular/core';
import {FastenApiService} from '../../services/fasten-api.service';
import {Source} from '../../models/fasten/source';
import {Source} from '../../../lib/models/database/source';
import {Router} from '@angular/router';
import {Summary} from '../../models/fasten/summary';
import {ResourceTypeCounts} from '../../models/fasten/source-summary';
import {ResourceFhir} from '../../models/fasten/resource_fhir';
import {ResourceFhir} from '../../../lib/models/database/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';
@Component({
selector: 'app-dashboard',
@ -22,7 +23,11 @@ export class DashboardComponent implements OnInit {
metadataSource: { [name: string]: MetadataSource }
constructor(private fastenApi: FastenApiService, private router: Router) { }
constructor(
private fastenApi: FastenApiService,
private fastenDb: FastenDbService,
private router: Router
) { }
ngOnInit() {
@ -44,12 +49,12 @@ export class DashboardComponent implements OnInit {
// })
// })
forkJoin([this.fastenApi.getSummary(), this.fastenApi.getMetadataSources()]).subscribe(results => {
forkJoin([this.fastenDb.GetSummary(), this.fastenApi.GetMetadataSources()]).subscribe(results => {
let summary = results[0] as Summary
let metadataSource = results[1] as { [name: string]: MetadataSource }
//process
console.log(summary);
console.log("SUMMARY RESPONSE",summary);
this.sources = summary.sources
this.metadataSource = metadataSource
this.metadataSource["manual"] = {
@ -59,7 +64,6 @@ export class DashboardComponent implements OnInit {
"enabled": true,
}
//calculate the number of records
summary.resource_type_counts.forEach((resourceTypeInfo) => {
this.recordsCount += resourceTypeInfo.count
@ -71,16 +75,13 @@ export class DashboardComponent implements OnInit {
summary.patients.forEach((resourceFhir) => {
this.patientForSource[resourceFhir.source_id] = resourceFhir
})
});
}
selectSource(selectedSource: Source){
this.router.navigateByUrl(`/source/${selectedSource.id}`, {
this.router.navigateByUrl(`/source/${Base64.Encode(selectedSource._id)}`, {
state: selectedSource
});
}

View File

@ -23,9 +23,9 @@
<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">
<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>
<img [src]="'assets/sources/'+sourceInfo?.metadata['source_type']+'.png'" alt="client" 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>
</div>
</div>
@ -39,7 +39,7 @@
<div class="row row-sm">
<div class="col-lg">
<ngx-dropzone [multiple]="false" (change)="uploadSourceBundle($event)" accept=".json">
<ngx-dropzone [multiple]="false" (change)="uploadSourceBundleHandler($event)" accept=".json">
<ngx-dropzone-label>Select your EMR/EHR bundle. Must be in JSON format</ngx-dropzone-label>
<ngx-dropzone-preview *ngFor="let f of uploadedFile" [removable]="false">
<ngx-dropzone-label>{{ f.name }} ({{ f.type }})</ngx-dropzone-label>
@ -57,13 +57,13 @@
<div class="row row-sm">
<div *ngFor="let sourceData of availableSourceList" (click)="connect($event, sourceData['source_type'])" class="col-sm-3 mg-b-20 px-3">
<div class="card h-100 d-flex align-items-center justify-content-center p-3 rounded-0 cursor-pointer" [ngClass]="{'card-disable': !sourceData.enabled}">
<div *ngFor="let sourceData of availableSourceList" (click)="connectHandler($event, sourceData.metadata.source_type)" 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" [ngClass]="{'card-disable': !sourceData.metadata.enabled}">
<div class="card-body">
<img [src]="'assets/sources/'+sourceData['source_type']+'.png'" [alt]="metadataSources[sourceData['source_type']].display" class="img-fluid">
<img [src]="'assets/sources/'+sourceData.metadata.source_type+'.png'" [alt]="metadataSources[sourceData.metadata.source_type].display" class="img-fluid">
<div *ngIf="status[sourceData['source_type']]" class="progress">
<div [style.width]="status[sourceData['source_type']] == 'authorize' ? '33%' : '66%'" class="bg-indigo progress-bar progress-bar-striped progress-bar-animated" role="progressbar"></div>
<div *ngIf="status[sourceData.metadata.source_type]" class="progress">
<div [style.width]="status[sourceData.metadata.source_type] == 'authorize' ? '33%' : '66%'" class="bg-indigo progress-bar progress-bar-striped progress-bar-animated" role="progressbar"></div>
</div>
</div>
</div>
@ -79,7 +79,7 @@
<ng-template #contentModalRef let-modal>
<div class="modal-header">
<h4 class="modal-title" id="modal-basic-title">{{modalSourceInfo.metadata["display"]}}</h4>
<h4 class="modal-title" id="modal-basic-title">{{modalSelectedSourceListItem?.metadata["display"]}}</h4>
<button type="button" class="btn btn-close" aria-label="Close" (click)="modal.dismiss('Cross click')">
<span aria-hidden="true">×</span>
</button>
@ -96,8 +96,8 @@
</div>
<div class="modal-footer">
<button (click)="syncSource(modalSourceInfo.source)" type="button" class="btn btn-indigo">Sync</button>
<button (click)="connect($event, modalSourceInfo.source['source_type'])" type="button" class="btn btn-outline-light">Reconnect</button>
<button (click)="sourceSyncHandler(modalSelectedSourceListItem.source)" type="button" class="btn btn-indigo">Sync</button>
<button (click)="connectHandler($event, modalSelectedSourceListItem.source['source_type'])" type="button" class="btn btn-outline-light">Reconnect</button>
<button type="button" class="btn btn-outline-danger">Delete</button>
<button (click)="modal.dismiss('Close click')" type="button" class="btn btn-outline-light">Close</button>
</div>

View File

@ -1,23 +1,31 @@
import {Component, HostListener, OnInit} from '@angular/core';
import {Component, OnInit} from '@angular/core';
import {LighthouseService} from '../../services/lighthouse.service';
import {FastenApiService} from '../../services/fasten-api.service';
import {LighthouseSourceMetadata} from '../../models/lighthouse/lighthouse-source-metadata';
import * as Oauth from '@panva/oauth4webapi';
import {AuthorizeClaim} from '../../models/lighthouse/authorize-claim';
import {Source} from '../../models/fasten/source';
import {FastenDbService} from '../../services/fasten-db.service';
import {LighthouseSourceMetadata} from '../../../lib/models/lighthouse/lighthouse-source-metadata';
import {Source} from '../../../lib/models/database/source';
import {getAccessTokenExpiration, jwtDecode} from 'fhirclient/lib/lib';
import BrowserAdapter from 'fhirclient/lib/adapters/BrowserAdapter';
import {Observable, of, throwError, fromEvent } from 'rxjs';
import {concatMap, delay, retryWhen, timeout, first, map, filter, catchError} from 'rxjs/operators';
import * as FHIR from "fhirclient"
import {MetadataSource} from '../../models/fasten/metadata-source';
import {NgbModal, ModalDismissReasons} from '@ng-bootstrap/ng-bootstrap';
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';
// If you dont import this angular will import the wrong "Location"
export const sourceConnectWindowTimeout = 24*5000 //wait 2 minutes (5 * 24 = 120)
export class SourceListItem {
source?: Source
metadata: MetadataSource
}
@Component({
selector: 'app-medical-sources',
templateUrl: './medical-sources.component.html',
@ -28,25 +36,28 @@ export class MedicalSourcesComponent implements OnInit {
constructor(
private lighthouseApi: LighthouseService,
private fastenApi: FastenApiService,
private fastenDb: FastenDbService,
private modalService: NgbModal,
private route: ActivatedRoute,
private router: Router,
private location: Location,
private queueService: QueueService,
private toastService: ToastService
) { }
status: { [name: string]: string } = {}
metadataSources: {[name:string]: MetadataSource} = {}
connectedSourceList:any[] = []
availableSourceList:MetadataSource[] = []
connectedSourceList: SourceListItem[] = [] //source's are populated for this list
availableSourceList: SourceListItem[] = []
uploadedFile: File[] = []
closeResult = '';
modalSourceInfo:any = null;
modalSelectedSourceListItem:SourceListItem = null;
ngOnInit(): void {
this.fastenApi.getMetadataSources().subscribe((metadataSources: {[name:string]: MetadataSource}) => {
this.fastenApi.GetMetadataSources().subscribe((metadataSources: {[name:string]: MetadataSource}) => {
this.metadataSources = metadataSources
const callbackSourceType = this.route.snapshot.paramMap.get('source_type')
@ -54,8 +65,9 @@ export class MedicalSourcesComponent implements OnInit {
this.callback(callbackSourceType).then(console.log)
}
this.fastenApi.getSources()
.subscribe((sourceList: Source[]) => {
this.fastenDb.GetSources()
.then((paginatedList) => {
const sourceList = paginatedList.rows as Source[]
for (const sourceType in this.metadataSources) {
let isConnected = false
@ -69,7 +81,7 @@ export class MedicalSourcesComponent implements OnInit {
if(!isConnected){
//this source has not been found in the connected list, lets add it to the available list.
this.availableSourceList.push(this.metadataSources[sourceType])
this.availableSourceList.push({metadata: this.metadataSources[sourceType]})
}
}
@ -79,12 +91,17 @@ export class MedicalSourcesComponent implements OnInit {
}
connect($event: MouseEvent, sourceType: string) {
/**
* after pressing the logo (connectHandler button), this function will generate an authorize url for this source, and redirec the user.
* @param $event
* @param sourceType
*/
public connectHandler($event: MouseEvent, sourceType: string):void {
($event.currentTarget as HTMLButtonElement).disabled = true;
this.status[sourceType] = "authorize"
this.lighthouseApi.getLighthouseSource(sourceType)
.subscribe(async (sourceMetadata: LighthouseSourceMetadata) => {
.then(async (sourceMetadata: LighthouseSourceMetadata) => {
console.log(sourceMetadata);
let authorizationUrl = await this.lighthouseApi.generateSourceAuthorizeUrl(sourceType, sourceMetadata)
@ -95,11 +112,15 @@ export class MedicalSourcesComponent implements OnInit {
});
}
async callback(sourceType: string) {
/**
* if the user is redirected to this page from the lighthouse, we'll need to process the "code" to retrieve the access token & refresh token.
* @param sourceType
*/
public async callback(sourceType: string) {
//get the source metadata again
await this.lighthouseApi.getLighthouseSource(sourceType)
.subscribe(async (sourceMetadata: LighthouseSourceMetadata) => {
.then(async (sourceMetadata: LighthouseSourceMetadata) => {
//get required parameters from the URI and local storage
const callbackUrlParts = new URL(window.location.href)
@ -145,90 +166,123 @@ export class MedicalSourcesComponent implements OnInit {
//Create FHIR Client
const sourceCredential: Source = {
source_type: sourceType,
oauth_authorization_endpoint: sourceMetadata.authorization_endpoint,
oauth_token_endpoint: sourceMetadata.token_endpoint,
oauth_registration_endpoint: "",
oauth_introspection_endpoint: sourceMetadata.introspection_endpoint,
oauth_userinfo_endpoint: sourceMetadata.userinfo_endpoint,
oauth_token_endpoint_auth_methods_supported: "",
const dbSourceCredential = new Source({
source_type: sourceType as SourceType,
authorization_endpoint: sourceMetadata.authorization_endpoint,
token_endpoint: sourceMetadata.token_endpoint,
introspection_endpoint: sourceMetadata.introspection_endpoint,
userinfo_endpoint: sourceMetadata.userinfo_endpoint,
api_endpoint_base_url: sourceMetadata.api_endpoint_base_url,
client_id: sourceMetadata.client_id,
redirect_uri: sourceMetadata.redirect_uri,
scopes: sourceMetadata.scopes_supported ? sourceMetadata.scopes_supported.join(' ') : undefined,
patient_id: payload.patient,
scopes_supported: sourceMetadata.scopes_supported,
issuer: sourceMetadata.issuer,
grant_types_supported: sourceMetadata.grant_types_supported,
response_types_supported: sourceMetadata.response_types_supported,
aud: sourceMetadata.aud,
code_challenge_methods_supported: sourceMetadata.code_challenge_methods_supported,
confidential: sourceMetadata.confidential,
cors_relay_required: sourceMetadata.cors_relay_required,
patient: payload.patient,
access_token: payload.access_token,
refresh_token: payload.refresh_token,
id_token: payload.id_token,
code_challenge: "",
code_verifier: "",
// @ts-ignore - in some cases the getAccessTokenExpiration is a string, which cases failures to store Source in db.
expires_at: parseInt(getAccessTokenExpiration(payload, new BrowserAdapter())),
confidential: sourceMetadata.confidential
}
})
await this.fastenApi.createSource(sourceCredential).subscribe(
(respData) => {
delete this.status[sourceType]
// window.location.reload();
await this.fastenDb.UpsertSource(dbSourceCredential).then(console.log)
this.queueSourceSyncWorker(sourceType as SourceType, dbSourceCredential)
console.log("source credential create response:", respData)
//remove item from available sources list, add to connected sources.
this.availableSourceList.splice(this.availableSourceList.indexOf(this.metadataSources[sourceType]), 1);
this.connectedSourceList.push({source: respData, metadata: this.metadataSources[sourceType]})
},
(err) => {
delete this.status[sourceType]
// window.location.reload();
console.log(err)
}
)
})
}
uploadSourceBundle(event) {
/**
* this function is used to process manually "uploaded" FHIR bundle files, adding them to the database.
* @param event
*/
public uploadSourceBundleHandler(event) {
this.uploadedFile = [event.addedFiles[0]]
this.fastenApi.createManualSource(event.addedFiles[0]).subscribe(
(respData) => {
console.log("source manual source create response:", respData)
},
(err) => {console.log(err)},
() => {
this.uploadedFile = []
}
)
//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 = []
// }
// )
}
openModal(contentModalRef, sourceInfo: any) {
this.modalSourceInfo = sourceInfo
let modalSourceInfo = this.modalSourceInfo
public openModal(contentModalRef, sourceListItem: SourceListItem) {
this.modalSelectedSourceListItem = sourceListItem
this.modalService.open(contentModalRef, {ariaLabelledBy: 'modal-basic-title'}).result.then((result) => {
modalSourceInfo = null
this.modalSelectedSourceListItem = null
this.closeResult = `Closed with: ${result}`;
}, (reason) => {
modalSourceInfo = null
this.modalSelectedSourceListItem = null
this.closeResult = `Dismissed ${this.getDismissReason(reason)}`;
});
}
syncSource(source: Source){
public sourceSyncHandler(source: Source){
this.status[source.source_type] = "authorize"
this.modalService.dismissAll()
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)
}
)
this.queueSourceSyncWorker(source.source_type as SourceType, source)
}
///////////////////////////////////////////////////////////////////////////////////////
// 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 {

View File

@ -3,11 +3,11 @@
<div class="az-content-body">
<div class="az-content-breadcrumb">
<span>Resource</span>
<span>{{resource.source_resource_type}}</span>
<span>{{resource.source_resource_id}}</span>
<span>{{resource?.source_resource_type}}</span>
<span>{{resource?.source_resource_id}}</span>
</div>
<pre *ngIf="resource"><code [highlight]="resource.payload | json"></code></pre>
<pre *ngIf="resource"><code [highlight]="resource.resource_raw | json"></code></pre>
</div><!-- az-content-body -->
</div>

View File

@ -1,8 +1,8 @@
import { Component, OnInit } from '@angular/core';
import {FastenApiService} from '../../services/fasten-api.service';
import {FastenDbService} from '../../services/fasten-db.service';
import {ActivatedRoute, Router} from '@angular/router';
import {Source} from '../../models/fasten/source';
import {ResourceFhir} from '../../models/fasten/resource_fhir';
import {ResourceFhir} from '../../../lib/models/database/resource_fhir';
import {Base64} from '../../../lib/utils/base64';
@Component({
selector: 'app-resource-detail',
@ -13,14 +13,15 @@ export class ResourceDetailComponent implements OnInit {
resource: ResourceFhir = null
constructor(private fastenApi: FastenApiService, private router: Router, private route: ActivatedRoute) {
constructor(private fastenDb: FastenDbService, private router: Router, private route: ActivatedRoute) {
}
ngOnInit(): void {
//always request the resource by id
this.fastenApi.getResourceBySourceId(this.route.snapshot.paramMap.get('source_id'), this.route.snapshot.paramMap.get('resource_id')).subscribe((resourceFhir) => {
this.resource = resourceFhir;
});
this.fastenDb.GetResource(Base64.Decode(this.route.snapshot.paramMap.get('resource_id')))
.then((resourceFhir) => {
this.resource = resourceFhir;
});
}
}

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