working pagination.

added test recordings for logicahealth

CONTRIBUTING.md

@@ -3,5 +3,5 @@
 cd frontend 
 npm run dist
 go mod vendor
-go run backend/cmd/fasten/fasten.go start --config ./config.yaml
-```
+go run backend/cmd/fasten/fasten.go start --config ./config.yaml --debug
+```

backend/pkg/hub/internal/fhir/base/base_client.go

@@ -11,6 +11,7 @@ import (
 	"golang.org/x/oauth2"
 	"io"
 	"net/http"
+	"net/url"
 	"os"
 	"strings"
 	"time"
@@ -96,9 +97,26 @@ func NewBaseClient(ctx context.Context, appConfig config.Interface, globalLogger
 ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 // HttpClient
 ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-func (c *BaseClient) GetRequest(resourceSubpath string, decodeModelPtr interface{}) error {
-	url := fmt.Sprintf("%s/%s", strings.TrimRight(c.Source.ApiEndpointBaseUrl, "/"), strings.TrimLeft(resourceSubpath, "/"))
-	resp, err := c.OauthClient.Get(url)
+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
+	}
+	req.Header.Add("Accept", "application/json+fhir")
+
+	//resp, err := c.OauthClient.Get(url)
+	resp, err := c.OauthClient.Do(req)
 
 	if err != nil {
 		return err
@@ -106,7 +124,7 @@ func (c *BaseClient) GetRequest(resourceSubpath string, decodeModelPtr interface
 	defer resp.Body.Close()
 
 	if resp.StatusCode >= 300 || resp.StatusCode < 200 {
-		return fmt.Errorf("An error occurred during request %s - %d - %s", url, resp.StatusCode, resp.Status)
+		return fmt.Errorf("An error occurred during request %s - %d - %s", resourceUrl, resp.StatusCode, resp.Status)
 	}
 
 	err = ParseBundle(resp.Body, decodeModelPtr)

backend/pkg/hub/internal/fhir/base/fhir401_client.go

@@ -32,6 +32,39 @@ func (c *FHIR401Client) GetPatientBundle(patientId string) (fhir401.Bundle, erro
 	// https://www.hl7.org/fhir/patient-operation-everything.html
 	bundle := fhir401.Bundle{}
 	err := c.GetRequest(fmt.Sprintf("Patient/%s/$everything", patientId), &bundle)
+	if err != nil {
+		return bundle, err
+	}
+	var next string
+	var self string
+	for _, link := range bundle.Link {
+		if link.Relation == "next" {
+			next = link.Url
+		} else if link.Relation == "self" {
+			self = link.Url
+		}
+	}
+
+	for len(next) > 0 && next != self {
+		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 next pointer
+		self = ""
+		for _, link := range nextBundle.Link {
+			if link.Relation == "next" {
+				next = link.Url
+			} else if link.Relation == "self" {
+				self = link.Url
+			}
+		}
+	}
+
 	return bundle, err
 
 }

backend/pkg/hub/internal/fhir/logica/client_test.go

@@ -0,0 +1,49 @@
+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("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:         "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)
+}