Merge pull request #67 from neicnordic/test/unit-tests

WIP Test/unit tests

.github/workflows/test.yml

@@ -0,0 +1,40 @@
+name: Tests
+
+on: [push]
+
+jobs:
+
+  build:
+    name: Build
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        go-version: [1.16]
+    steps:
+
+      - name: Set up Go ${{ matrix.go-version }}
+        uses: actions/setup-go@v2
+        with:
+          go-version: ${{ matrix.go-version }}
+        id: go
+
+      - name: Check out code into the Go module directory
+        uses: actions/checkout@v2
+
+      - name: Get dependencies
+        run: |
+          go get -v -t -d ./...
+          if [ -f Gopkg.toml ]; then
+              curl https://raw.githubusercontent.com/golang/dep/master/install.sh | sh
+              dep ensure
+          fi
+      - name: Test
+        run: go test -v -coverprofile=coverage.txt -covermode=atomic ./...
+
+      - name: Codecov
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage.txt
+          flags: unittests
+          fail_ci_if_error: false

KNOWN_ISSUES.md

@@ -0,0 +1,13 @@
+# Known Issues and Troubleshooting
+
+## Files metadata endpoint doesn't work with visas
+If using GA4GH Visas with `/metadata/datasets/{dataset}/files`, e.g. `/metadata/datasets/https://doi.org/abc/123/files`, a reverse proxy might remove adjacent slashes `//`->`/`.
+This has been observed with nginx, with a fix as follows:
+
+[disable slash merging](http://nginx.org/en/docs/http/ngx_http_core_module.html#merge_slashes)
+in `server` context
+```
+server {
+    merge_slashes off
+}
+```

README.md

@@ -1,3 +1,8 @@
+[![CodeQL](https://github.com/neicnordic/sda-download/actions/workflows/codeql-analysis.yml/badge.svg)](https://github.com/neicnordic/sda-download/actions/workflows/codeql-analysis.yml)
+[![Tests](https://github.com/neicnordic/sda-download/actions/workflows/test.yml/badge.svg)](https://github.com/neicnordic/sda-download/actions/workflows/test.yml)
+[![Multilinters](https://github.com/neicnordic/sda-download/actions/workflows/report.yml/badge.svg)](https://github.com/neicnordic/sda-download/actions/workflows/report.yml)
+[![codecov](https://codecov.io/gh/neicnordic/sda-download/branch/main/graph/badge.svg?token=ZHO4XCDPJO)](https://codecov.io/gh/neicnordic/sda-download)
+
 # SDA Download
 `sda-download` is a `go` implementation of the [Data Out API](https://neic-sda.readthedocs.io/en/latest/dataout.html#rest-api-endpoints). The [API Reference](docs/API.md) has example requests and responses.
 

api/api.go

@@ -6,6 +6,7 @@ import (
 	"net/http"
 	"time"
 
+	"github.com/gorilla/mux"
 	"github.com/neicnordic/sda-download/api/middleware"
 	"github.com/neicnordic/sda-download/api/sda"
 	"github.com/neicnordic/sda-download/internal/config"
@@ -16,11 +17,11 @@ import (
 func Setup() *http.Server {
 	// Set up routing
 	log.Info("(2/5) Registering endpoint handlers")
-	r := http.NewServeMux()
+	r := mux.NewRouter().SkipClean(true)
 
 	r.Handle("/metadata/datasets", middleware.TokenMiddleware(http.HandlerFunc(sda.Datasets)))
-	r.Handle("/metadata/datasets/", middleware.TokenMiddleware(http.HandlerFunc(sda.Files)))
-	r.Handle("/files/", middleware.TokenMiddleware(http.HandlerFunc(sda.Download)))
+	r.Handle("/metadata/datasets/{dataset:[A-Za-z0-9-_.~:/?#@!$&'()*+,;=]+}/files", middleware.TokenMiddleware(http.HandlerFunc(sda.Files)))
+	r.Handle("/files/{fileid}", middleware.TokenMiddleware(http.HandlerFunc(sda.Download)))
 
 	// Configure TLS settings
 	log.Info("(3/5) Configuring TLS")

api/api_test.go

@@ -0,0 +1,27 @@
+package api
+
+import (
+	"crypto/tls"
+	"testing"
+
+	"github.com/neicnordic/sda-download/internal/config"
+)
+
+func TestSetup(t *testing.T) {
+
+	// Create web server app
+	config.Config.App.Host = "localhost"
+	config.Config.App.Port = 8080
+	server := Setup()
+
+	// Verify that TLS is configured and set for minimum suggested version
+	if server.TLSConfig.MinVersion < tls.VersionTLS12 {
+		t.Errorf("server TLS version is too low, expected=%d, got=%d", tls.VersionTLS12, server.TLSConfig.MinVersion)
+	}
+
+	// Verify that server address is correctly read from config
+	expectedAddress := "localhost:8080"
+	if server.Addr != expectedAddress {
+		t.Errorf("server address was not correctly formed, expected=%s, received=%s", expectedAddress, server.Addr)
+	}
+}

api/middleware/middleware.go

@@ -48,12 +48,7 @@ func TokenMiddleware(nextHandler http.Handler) http.Handler {
 			}
 
 			// Get permissions
-			datasets, err = auth.GetPermissions(*visas)
-			if err != nil {
-				log.Errorf("failed to parse dataset permission visas, %s", err)
-				http.Error(w, "visa parsing failed", 500)
-				return
-			}
+			datasets = auth.GetPermissions(*visas)
 			if len(datasets) == 0 {
 				log.Debug("token carries no dataset permissions matching the database")
 				http.Error(w, "no datasets found", 404)
@@ -94,7 +89,7 @@ func storeDatasets(ctx context.Context, datasets []string) context.Context {
 }
 
 // GetDatasets extracts the dataset list from the request context
-func GetDatasets(ctx context.Context) []string {
+var GetDatasets = func(ctx context.Context) []string {
 	datasets := ctx.Value("datasets")
 	if datasets == nil {
 		log.Debug("request datasets context is empty")