added test to verify that wizard resource creation works correctly.

update fasten-sources (contains fix for silently ignoring failures during wizard resource creation). fixed file upload error in wizard. Fixed data structure error in wizard for DocumentReference. fixes #393
2024-01-26 22:01:34 -08:00 · 2024-01-26 22:01:34 -08:00 · 870f6ffee2
parent 1b3e43556e
commit 870f6ffee2
10 changed files with 228 additions and 16 deletions
--- a/backend/pkg/web/handler/account.go
+++ b/backend/pkg/web/handler/account.go
@ -8,7 +8,7 @@ import (
 	"net/http"
 )

-// SECURITY: this is a secure endpoint, and should only be called after a double confirmation
+// UX: this is a secure endpoint, and should only be called after a double confirmation
 func DeleteAccount(c *gin.Context) {
 	logger := c.MustGet(pkg.ContextKeyTypeLogger).(*logrus.Entry)
 	databaseRepo := c.MustGet(pkg.ContextKeyTypeDatabase).(database.DatabaseRepository)
--- a/backend/pkg/web/handler/resource_related_test.go
+++ b/backend/pkg/web/handler/resource_related_test.go
@ -0,0 +1,143 @@
+package handler
+
+import (
+	"bytes"
+	"context"
+	"encoding/json"
+	"fmt"
+	"github.com/fastenhealth/fasten-onprem/backend/pkg"
+	mock_config "github.com/fastenhealth/fasten-onprem/backend/pkg/config/mock"
+	"github.com/fastenhealth/fasten-onprem/backend/pkg/database"
+	"github.com/fastenhealth/fasten-onprem/backend/pkg/event_bus"
+	"github.com/fastenhealth/fasten-onprem/backend/pkg/models"
+	"github.com/gin-gonic/gin"
+	"github.com/golang/mock/gomock"
+	"github.com/sirupsen/logrus"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+	"github.com/stretchr/testify/suite"
+	"io"
+	"io/ioutil"
+	"log"
+	"mime/multipart"
+	"net/http"
+	"net/http/httptest"
+	"os"
+	"testing"
+)
+
+// Go through this page to understand how this file is structured.
+// https://pkg.go.dev/github.com/stretchr/testify/suite#section-documentation
+
+// Define the suite, and absorb the built-in basic suite
+// functionality from testify - including a T() method which
+// returns the current testing context
+type ResourceRelatedHandlerTestSuite struct {
+	suite.Suite
+	MockCtrl     *gomock.Controller
+	TestDatabase *os.File
+
+	AppConfig     *mock_config.MockInterface
+	AppRepository database.DatabaseRepository
+	AppEventBus   event_bus.Interface
+}
+
+// BeforeTest has a function to be executed right before the test starts and receives the suite and test names as input
+func (suite *ResourceRelatedHandlerTestSuite) BeforeTest(suiteName, testName string) {
+	suite.MockCtrl = gomock.NewController(suite.T())
+
+	dbFile, err := ioutil.TempFile("", fmt.Sprintf("%s.*.db", testName))
+	if err != nil {
+		log.Fatal(err)
+	}
+	suite.TestDatabase = dbFile
+
+	appConfig := mock_config.NewMockInterface(suite.MockCtrl)
+	appConfig.EXPECT().GetString("database.location").Return(suite.TestDatabase.Name()).AnyTimes()
+	appConfig.EXPECT().GetString("database.type").Return("sqlite").AnyTimes()
+	appConfig.EXPECT().IsSet("database.encryption.key").Return(false).AnyTimes()
+	appConfig.EXPECT().GetString("log.level").Return("INFO").AnyTimes()
+	suite.AppConfig = appConfig
+
+	appRepo, err := database.NewRepository(suite.AppConfig, logrus.WithField("test", suite.T().Name()), event_bus.NewNoopEventBusServer())
+	suite.AppRepository = appRepo
+
+	suite.AppEventBus = event_bus.NewNoopEventBusServer()
+
+	appRepo.CreateUser(context.Background(), &models.User{
+		Username: "test_username",
+		Password: "test",
+	})
+
+}
+
+// AfterTest has a function to be executed right after the test finishes and receives the suite and test names as input
+func (suite *ResourceRelatedHandlerTestSuite) AfterTest(suiteName, testName string) {
+	suite.MockCtrl.Finish()
+	os.Remove(suite.TestDatabase.Name())
+}
+
+// In order for 'go test' to run this suite, we need to create
+// a normal test function and pass our suite to suite.Run
+func TestResourceRelatedHandlerTestSuite(t *testing.T) {
+	suite.Run(t, new(ResourceRelatedHandlerTestSuite))
+}
+
+func (suite *ResourceRelatedHandlerTestSuite) TestResourceRelatedHandlerTestSuite() {
+	//setup
+	w := httptest.NewRecorder()
+	ctx, _ := gin.CreateTestContext(w)
+	ctx.Set(pkg.ContextKeyTypeLogger, logrus.WithField("test", suite.T().Name()))
+	ctx.Set(pkg.ContextKeyTypeDatabase, suite.AppRepository)
+	ctx.Set(pkg.ContextKeyTypeConfig, suite.AppConfig)
+	ctx.Set(pkg.ContextKeyTypeEventBusServer, suite.AppEventBus)
+	ctx.Set(pkg.ContextKeyTypeAuthUsername, "test_username")
+
+	//test
+	relatedJsonForm, relatedJsonWriter := createMultipartFormData(suite.T(), "file", "testdata/related.json") // just pass the file name
+	relatedReq, err := http.NewRequest("POST", "/api/v1/resource/related", &relatedJsonForm)
+	// set the content type, this will contain the boundary.
+	relatedReq.Header.Set("Content-Type", relatedJsonWriter.FormDataContentType())
+	ctx.Request = relatedReq
+	require.NoError(suite.T(), err)
+
+	CreateRelatedResources(ctx)
+
+	var responseWrapper models.ResponseWrapper
+	err = json.Unmarshal(w.Body.Bytes(), &responseWrapper)
+	require.NoError(suite.T(), err)
+
+	summary := responseWrapper.Data.(map[string]interface{})
+
+	//assert
+	assert.EqualValues(suite.T(), http.StatusOK, w.Code)
+	assert.Equal(suite.T(), summary["TotalResources"], 3)
+
+}
+
+// https://stackoverflow.com/a/56696333/1157633
+func createMultipartFormData(t *testing.T, fieldName, fileName string) (bytes.Buffer, *multipart.Writer) {
+	var b bytes.Buffer
+	var err error
+	w := multipart.NewWriter(&b)
+	var fw io.Writer
+	file := mustOpen(fileName)
+	if fw, err = w.CreateFormFile(fieldName, file.Name()); err != nil {
+		t.Errorf("Error creating writer: %v", err)
+	}
+	if _, err = io.Copy(fw, file); err != nil {
+		t.Errorf("Error with io.Copy: %v", err)
+	}
+	w.Close()
+	return b, w
+}
+
+func mustOpen(f string) *os.File {
+	r, err := os.Open(f)
+	if err != nil {
+		pwd, _ := os.Getwd()
+		fmt.Println("PWD: ", pwd)
+		panic(err)
+	}
+	return r
+}
--- a/backend/pkg/web/handler/testdata/related.json
+++ b/backend/pkg/web/handler/testdata/related.json
@ -0,0 +1,69 @@
+{
+  "resourceType": "List",
+  "entry": [],
+  "encounter": {
+    "reference": "Encounter/4e4e6346-2350-47c0-ba73-ee0fdaf3a8a7"
+  },
+  "contained": [
+    {
+      "resourceType": "Encounter",
+      "id": "4e4e6346-2350-47c0-ba73-ee0fdaf3a8a7",
+      "serviceType": {
+        "id": "562",
+        "identifier": [
+          {
+            "system": "http://terminology.hl7.org/CodeSystem/service-type",
+            "code": "562",
+            "display": "Test Message"
+          }
+        ],
+        "text": "Test Message"
+      },
+      "status": "finished",
+      "participant": [],
+      "period": {
+        "start": "2024-01-04T08:00:00.000Z",
+        "end": "2024-01-27T08:00:00.000Z"
+      },
+      "reasonReference": [],
+      "serviceProvider": {}
+    },
+    {
+      "id": "4e2611e4-df0d-4dae-ad32-1c90537b32af",
+      "resourceType": "Binary",
+      "contentType": "application/pdf",
+      "data": "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"
+    },
+    {
+      "id": "53066674-9e89-41e9-95d9-8eaf24b41ea6",
+      "resourceType": "DocumentReference",
+      "status": "current",
+      "category": [
+        {
+          "coding": [
+            {
+              "system": "http://loinc.org",
+              "code": "11488-4",
+              "display": "Consult Note"
+            }
+          ],
+          "text": "Consult Note"
+        }
+      ],
+      "content": [
+        {
+          "attachment": {
+            "contentType": "application/pdf",
+            "url": "urn:uuid:4e2611e4-df0d-4dae-ad32-1c90537b32af",
+            "title": "test attachment"
+          }
+        }
+      ],
+      "context": {
+        "encounter": [{
+          "reference": "Encounter/4e4e6346-2350-47c0-ba73-ee0fdaf3a8a7"
+        }]
+      }
+    }
+  ]
+}
--- a/frontend/src/app/components/medical-record-wizard-add-attachment/medical-record-wizard-add-attachment.component.html
+++ b/frontend/src/app/components/medical-record-wizard-add-attachment/medical-record-wizard-add-attachment.component.html
@ -30,7 +30,7 @@
      </div><!-- col -->
      <div class="col-6 mg-t-10 mg-lg-t-0 mg-l-10">
        <label for="customFile" class="custom-file-label">{{newAttachmentForm.get('file_name').value || 'Choose file'}}</label>
-        <input id="customFile" (change)="onAttachmentFileChange($event)" class="custom-file-input" formControlName="file_name" type="file">
+        <input id="customFile" (change)="onAttachmentFileChange($event)" class="custom-file-input" type="file">
      </div><!-- col -->
    </ng-container>
  </div>
--- a/frontend/src/app/components/medical-record-wizard-add-attachment/medical-record-wizard-add-attachment.component.ts
+++ b/frontend/src/app/components/medical-record-wizard-add-attachment/medical-record-wizard-add-attachment.component.ts
@ -41,15 +41,16 @@ export class MedicalRecordWizardAddAttachmentComponent implements OnInit {
    console.log("onAttachmentFileChange")
    let fileInput = $event.target as HTMLInputElement;
    if (fileInput.files && fileInput.files[0]) {
+      let processingFile = fileInput.files[0]
      let reader = new FileReader();
      reader.onloadend = () => {
        // use a regex to remove data url part
        const base64String = (reader.result as string).replace('data:', '').replace(/^.+,/, '');
        this.newAttachmentForm.get('file_content').setValue(base64String)
      };
-      reader.readAsDataURL(fileInput.files[0]);
-      this.newAttachmentForm.get('file_name').setValue(fileInput.files[0].name)
-      this.newAttachmentForm.get('file_size').setValue(fileInput.files[0].size)
+      reader.readAsDataURL(processingFile);
+      this.newAttachmentForm.get('file_name').setValue(processingFile.name)
+      this.newAttachmentForm.get('file_size').setValue(processingFile.size)
    }
  }

--- a/frontend/src/app/components/medical-record-wizard/medical-record-wizard.utilities.ts
+++ b/frontend/src/app/components/medical-record-wizard/medical-record-wizard.utilities.ts
@ -371,13 +371,12 @@ function resourceAttachmentToR4DocumentReference(resourceStorage: ResourceStorag
        }
      }
    ],
-    context: [
-      {
-        encounter: {
+    context: {
+      encounter: [{
        reference: generateReferenceUriFromResourceOrReference(encounterResource) //Encounter
-        },
+      }],
    }
-    ]
+
    // date: `${new Date(resourceDocumentReference.date.year,resourceDocumentReference.date.month-1,resourceDocumentReference.date.day).toISOString()}`,
  } as DocumentReference
  resourceStorage['DocumentReference'][documentReferenceResource.id] = documentReferenceResource
--- a/frontend/src/app/pages/medical-sources/medical-sources.component.html
+++ b/frontend/src/app/pages/medical-sources/medical-sources.component.html
@ -19,7 +19,7 @@
          <br/>
          <br/>
        In <strong>Sandbox mode</strong> Fasten Health cannot access real patient information. You must use Sandbox credentials when authenticating to healthcare sources.
-          <a href="https://github.com/fastenhealth/docs/blob/main/BETA.md#connecting-a-new-source" externalLink>These credentials are available on Github</a>
+          <a href="https://docs.fastenhealth.com/getting-started/sandbox.html#connecting-a-new-source" externalLink>These credentials are available in our Sandbox Guide</a>
        </span>
      </div>

--- a/frontend/src/assets/favicon/android-chrome-300x300.png
+++ b/frontend/src/assets/favicon/android-chrome-300x300.png
--- a/go.mod
+++ b/go.mod
@ -15,7 +15,7 @@ require (
 	github.com/dave/jennifer v1.6.1
 	github.com/dominikbraun/graph v0.15.0
 	github.com/dop251/goja v0.0.0-20230605162241-28ee0ee714f3
-	github.com/fastenhealth/fasten-sources v0.5.5
+	github.com/fastenhealth/fasten-sources v0.5.6
 	github.com/fastenhealth/gofhir-models v0.0.6
 	github.com/gin-gonic/gin v1.9.0
 	github.com/go-gormigrate/gormigrate/v2 v2.1.1
--- a/go.sum
+++ b/go.sum
@ -101,8 +101,8 @@ github.com/envoyproxy/go-control-plane v0.9.4/go.mod h1:6rpuAdCZL397s3pYoYcLgu1m
 github.com/envoyproxy/go-control-plane v0.9.7/go.mod h1:cwu0lG7PUMfa9snN8LXBig5ynNVH9qI8YYLbd1fK2po=
 github.com/envoyproxy/go-control-plane v0.9.9-0.20201210154907-fd9021fe5dad/go.mod h1:cXg6YxExXjJnVBQHBLXeUAgxn2UodCpnH306RInaBQk=
 github.com/envoyproxy/protoc-gen-validate v0.1.0/go.mod h1:iSmxcyjqTsJpI2R4NaDN7+kN2VEUnK/pcBlmesArF7c=
-github.com/fastenhealth/fasten-sources v0.5.5 h1:+vOIG7R/J7QxEZrrfPFfaBzqYU5eDu7x/bc/cgOjvW4=
-github.com/fastenhealth/fasten-sources v0.5.5/go.mod h1:hUQATAu5KrxKbACJoVt4iEKIGnRtmiOmHz+5TLfyiCM=
+github.com/fastenhealth/fasten-sources v0.5.6 h1:F4Qmw9ABLSkqkWncoSnChBRDVWLrzkJv+z4z/Ue/fdc=
+github.com/fastenhealth/fasten-sources v0.5.6/go.mod h1:hUQATAu5KrxKbACJoVt4iEKIGnRtmiOmHz+5TLfyiCM=
 github.com/fastenhealth/gofhir-models v0.0.6 h1:yJYYaV1eJtHiGEfA1rXLsyOm/9hIi6s2cGoZzGfW1tM=
 github.com/fastenhealth/gofhir-models v0.0.6/go.mod h1:xB8ikGxu3bUq2b1JYV+CZpHqBaLXpOizFR0eFBCunis=
 github.com/fatih/color v1.7.0/go.mod h1:Zm6kSWBoL9eyXnKyktHP6abPY2pDugNf5KwzbycvMj4=