Merge branch 'samply:main' into rennkater-patch-1

Author: rennkater

.github/workflows/build.yml

@@ -41,7 +41,7 @@ jobs:
         go-version-file: go.mod
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@e296a935590eb16afc0c0108289f68c87e2a89a5 # v4
+      uses: github/codeql-action/init@014f16e7ab1402f30e7c3329d33797e7948572db # v4
       with:
         languages: go
 
@@ -60,7 +60,7 @@ jobs:
       run: go build .
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@e296a935590eb16afc0c0108289f68c87e2a89a5 # v4
+      uses: github/codeql-action/analyze@014f16e7ab1402f30e7c3329d33797e7948572db # v4
 
     - name: Upload Binary
       uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
@@ -122,7 +122,7 @@ jobs:
       run: go build .
 
     - name: Generate SBOM
-      uses: anchore/sbom-action@f8bdd1d8ac5e901a77a92f111440fdb1b593736b # v0
+      uses: anchore/sbom-action@8e94d75ddd33f69f691467e42275782e4bfefe84 # v0
       with:
         syft-version: 'v1.29.0'
         artifact-name: blazectl-${{ matrix.os }}-${{ matrix.arch }}-sbom.spdx.json
@@ -156,8 +156,9 @@ jobs:
       run: zip -q "blazectl-$VERSION-$OS-$ARCH.zip" blazectl.exe
 
     - name: Release
-      uses: softprops/action-gh-release@aec2ec56f94eb8180ceec724245f64ef008b89f5 # v2
+      uses: softprops/action-gh-release@5be0e66d93ac7ed76da52eca8bb058f665c3a5fe # v2
       with:
+        draft: true
         files: blazectl-*
 
   integration-test:

.github/workflows/scorecard.yml

@@ -58,6 +58,6 @@ jobs:
     # Upload the results to GitHub's code scanning dashboard (optional).
     # Commenting out will disable upload of results to your repo's Code Scanning dashboard
     - name: "Upload to code-scanning"
-      uses: github/codeql-action/upload-sarif@e296a935590eb16afc0c0108289f68c87e2a89a5 # v4
+      uses: github/codeql-action/upload-sarif@014f16e7ab1402f30e7c3329d33797e7948572db # v4
       with:
         sarif_file: results.sarif

README.md

@@ -45,6 +45,7 @@ Available Commands:
   download-history Download history in NDJSON format
   evaluate-measure Evaluates a Measure
   help             Help about any command
+  render-report    Renders a MeasureReport
   upload           Upload transaction bundles
 
 Flags:
@@ -191,11 +192,19 @@ Given a measure in YAML form, creates the required FHIR resources, evaluates tha
 You can run:
 
 ```sh
-blazectl evaluate-measure --server "http://localhost:8080/fhir" stratifier-condition-code.yml
+blazectl evaluate-measure --server "http://localhost:8080/fhir" query.yml
 ```
 
 More comprehensive documentation can be found in the [Blaze CQL Queries Documentation][9].
 
+### Render Report
+
+Renders a FHIR MeasureReport resource as simple, standalone HTML file. The idea is to combine two `blazectl` calls, first the `evaluate-measure` call and second the `render-report` call. 
+
+```sh
+blazectl evaluate-measure --server "http://localhost:8080/fhir" query.yml | blazectl render-report > query.html
+```
+
 ## GitHub Attestations
 
 To ensure trust and security in the software supply chain, GitHub [attestations][11] are available for all `blazectl` binaries. To verify the attestations, please install the [GitHub CLI][10] tool and run:

cmd/compact.go

@@ -88,6 +88,7 @@ var compactCmd = &cobra.Command{
 			return err
 		}
 
+		fmt.Printf("Start compacting column family `%s` in database `%s`...\n", args[1], args[0])
 		req, err := client.NewPostSystemOperationRequest("compact", true, createParameters(args[0], args[1]))
 		if err != nil {
 			return err

cmd/evaluateMeasure.go

@@ -6,19 +6,20 @@ import (
 	"encoding/json"
 	"errors"
 	"fmt"
+	"io"
+	"net/http"
+	"net/url"
+	"os"
+	"os/signal"
+	"time"
+
 	"github.com/goccy/go-yaml"
 	"github.com/google/uuid"
 	"github.com/samply/blazectl/data"
 	"github.com/samply/blazectl/fhir"
 	"github.com/samply/blazectl/util"
 	fm "github.com/samply/golang-fhir-models/fhir-models/fhir"
 	"github.com/spf13/cobra"
-	"io"
-	"net/http"
-	"net/url"
-	"os"
-	"os/signal"
-	"time"
 )
 
 var forceSync bool
@@ -69,6 +70,12 @@ func createMeasureGroup(g data.Group) (*fm.MeasureGroup, error) {
 			},
 		}
 	}
+	if g.Code != "" {
+		group.Code = &fm.CodeableConcept{Text: &g.Code}
+	}
+	if g.Description != "" {
+		group.Description = &g.Description
+	}
 	for i, population := range g.Population {
 		p, err := createMeasureGroupPopulation(population)
 		if err != nil {
@@ -103,22 +110,26 @@ func createMeasureGroupPopulation(population data.Population) (*fm.MeasureGroupP
 	}, nil
 }
 
-func createMeasureGroupStratifier(stratifier data.Stratifier) (*fm.MeasureGroupStratifier, error) {
-	if stratifier.Code == "" {
+func createMeasureGroupStratifier(s data.Stratifier) (*fm.MeasureGroupStratifier, error) {
+	if s.Code == "" {
 		return nil, fmt.Errorf("missing code")
 	}
-	if stratifier.Expression == "" {
+	if s.Expression == "" {
 		return nil, fmt.Errorf("missing expression name")
 	}
-	return &fm.MeasureGroupStratifier{
+	stratifier := fm.MeasureGroupStratifier{
 		Code: &fm.CodeableConcept{
-			Text: &stratifier.Code,
+			Text: &s.Code,
 		},
 		Criteria: &fm.Expression{
 			Language:   "text/cql-identifier",
-			Expression: &stratifier.Expression,
+			Expression: &s.Expression,
 		},
-	}, nil
+	}
+	if s.Description != "" {
+		stratifier.Description = &s.Description
+	}
+	return &stratifier, nil
 }
 
 func createCoding(system string, code string) fm.Coding {

cmd/evalueMeasure_test.go

@@ -4,14 +4,15 @@ import (
 	"encoding/json"
 	"errors"
 	"fmt"
-	"github.com/samply/blazectl/data"
-	"github.com/samply/blazectl/fhir"
-	fm "github.com/samply/golang-fhir-models/fhir-models/fhir"
-	"github.com/stretchr/testify/assert"
 	"net/http"
 	"net/http/httptest"
 	"net/url"
 	"testing"
+
+	"github.com/samply/blazectl/data"
+	"github.com/samply/blazectl/fhir"
+	fm "github.com/samply/golang-fhir-models/fhir-models/fhir"
+	"github.com/stretchr/testify/assert"
 )
 
 func TestCreateMeasureResource(t *testing.T) {
@@ -106,6 +107,52 @@ func TestCreateMeasureResource(t *testing.T) {
 		assert.Equal(t, "InInitialPopulation", *resource.Group[0].Population[0].Criteria.Expression)
 	})
 
+	t.Run("with one group with code and one population", func(t *testing.T) {
+		m := data.Measure{
+			Group: []data.Group{
+				{
+					Code: "observation",
+					Population: []data.Population{
+						{
+							Expression: "InInitialPopulation",
+						},
+					},
+				},
+			},
+		}
+
+		resource, err := CreateMeasureResource(m, measureUrl, libraryUrl)
+		if err != nil {
+			t.Fatalf("error while generating the measure resource: %v", err)
+		}
+
+		assert.Equal(t, 1, len(resource.Group))
+		assert.Equal(t, "observation", *resource.Group[0].Code.Text)
+	})
+
+	t.Run("with one group with description and one population", func(t *testing.T) {
+		m := data.Measure{
+			Group: []data.Group{
+				{
+					Description: "all the observations",
+					Population: []data.Population{
+						{
+							Expression: "InInitialPopulation",
+						},
+					},
+				},
+			},
+		}
+
+		resource, err := CreateMeasureResource(m, measureUrl, libraryUrl)
+		if err != nil {
+			t.Fatalf("error while generating the measure resource: %v", err)
+		}
+
+		assert.Equal(t, 1, len(resource.Group))
+		assert.Equal(t, "all the observations", *resource.Group[0].Description)
+	})
+
 	t.Run("with one group and one population and one empty stratifier", func(t *testing.T) {
 		m := data.Measure{
 			Group: []data.Group{
@@ -185,6 +232,36 @@ func TestCreateMeasureResource(t *testing.T) {
 		assert.Equal(t, "foo", *resource.Group[0].Stratifier[0].Code.Text)
 	})
 
+	t.Run("with one group and one population and one stratifier with description", func(t *testing.T) {
+		m := data.Measure{
+			Group: []data.Group{
+				{
+					Population: []data.Population{
+						{
+							Expression: "InInitialPopulation",
+						},
+					},
+					Stratifier: []data.Stratifier{
+						{
+							Code:        "foo",
+							Description: "the foo stratifier",
+							Expression:  "Foo",
+						},
+					},
+				},
+			},
+		}
+
+		resource, err := CreateMeasureResource(m, measureUrl, libraryUrl)
+		if err != nil {
+			t.Fatalf("error while generating the measure resource: %v", err)
+		}
+
+		assert.Equal(t, 1, len(resource.Group))
+		assert.Equal(t, 1, len(resource.Group[0].Stratifier))
+		assert.Equal(t, "the foo stratifier", *resource.Group[0].Stratifier[0].Description)
+	})
+
 	t.Run("with one Condition group", func(t *testing.T) {
 		m := data.Measure{
 			Group: []data.Group{

cmd/renderReport.go

@@ -0,0 +1,70 @@
+// Copyright 2019 - 2025 The Samply Community
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package cmd
+
+import (
+	_ "embed"
+	"encoding/json"
+	"io"
+	"os"
+
+	"html/template"
+
+	fm "github.com/samply/golang-fhir-models/fhir-models/fhir"
+	"github.com/spf13/cobra"
+)
+
+//go:embed report-template.gohtml
+var reportTemplate string
+
+var renderReportCmd = &cobra.Command{
+	Use:   "render-report",
+	Short: "Renders a MeasureReport",
+	RunE: func(cmd *cobra.Command, args []string) error {
+		data, err := io.ReadAll(os.Stdin)
+		if err != nil {
+			return err
+		}
+
+		var report fm.MeasureReport
+		if err := json.Unmarshal(data, &report); err != nil {
+			return err
+		}
+
+		funcMap := template.FuncMap{
+			"inc": func(i int) int {
+				return i + 1
+			},
+			"ratio": func(n int, d int) float32 {
+				return float32(n*100) / float32(d)
+			},
+			"isNullString": func(s *string) bool {
+				return s == nil || *s == "null"
+			},
+		}
+
+		tmpl := template.Must(template.New("report").Funcs(funcMap).Parse(reportTemplate))
+
+		if err := tmpl.Execute(os.Stdout, report); err != nil {
+			return err
+		}
+
+		return nil
+	},
+}
+
+func init() {
+	rootCmd.AddCommand(renderReportCmd)
+}