Add support for Questionnaire to Structure Map Validation

README.md

@@ -6,11 +6,11 @@ A command line utility to support FHIRCore content authoring. This tool supports
 
 Download the latest release from https://github.com/opensrp/fhircore-tooling/releases
 
-To run it as a java jar use the command `java -jar efsity-1.0.0.jar -h` . This is the help command and will list the available options.
+To run it as a java jar by using the command `java -jar efsity-2.0.0.jar -h` . This is the help command and will list the available options.
 
 If you are using a linux environment e.g. bash you can choose to create an _alias_ for this as shown below. _(Remember to reload the terminal)_
 
-`alias fct='java -jar ~/Downloads/efsity-1.0.0.jar'`
+`alias fct='java -jar ~/Downloads/efsity-2.0.0.jar'`
 
 To run the previous help command you can then run `fct -h` in your terminal.
 
@@ -60,7 +60,12 @@ The above will output a list of errors and warnings based on any configuration r
 -c or --composition - the composition json file of the project
 -i or --input - the input directory path. This should point to the folder with the app configurations e.g. ~/Workspace/fhir-resources/ecbis_cha_preview/
 -o or --output - the output path, can be a file or directory. Optional - default is current directory
+-sm or --structure-maps - (Optional) the directory path to the location of structure map .txt or .map files. Must be a directory. Must be used with the -q flag
+-q or --questionnaires - (Optional) the directory path to the location of questionnaires .json files. Must be a directory. Must be used with the -sm flag
 ```
+
+**Note:** To include _Questionnaire_ and _Structure Map_ validation add the `-sm` and `-q` flags
+
 **Sample screenshot output**
 <br/>
 <img width="715" alt="Screenshot 2023-03-27 at 21 43 09" src="https://user-images.githubusercontent.com/10017086/228037581-209f9bab-d1b9-45eb-a920-aa12c70c5b98.png">

pom.xml

@@ -4,7 +4,7 @@
 
   <groupId>org.smartregister</groupId>
   <artifactId>fhircore-tooling</artifactId>
-  <version>1.0.0</version>
+  <version>2.0.0</version>
 
   <properties>
     <code.name>efsity</code.name>
@@ -118,22 +118,48 @@
     <dependency>
       <groupId>org.opencds.cqf.cql</groupId>
       <artifactId>evaluator</artifactId>
-      <version>${opencds.cql.version}</version>
+      <version>${cql.version}</version>
+      <exclusions>
+        <exclusion>
+          <groupId>ca.uhn.hapi.fhir</groupId>
+          <artifactId>org.hl7.fhir.r5</artifactId>
+        </exclusion>
+        <exclusion>
+          <groupId>ca.uhn.hapi.fhir</groupId>
+          <artifactId>org.hl7.fhir.dstu2</artifactId>
+        </exclusion>
+        <exclusion>
+          <groupId>ca.uhn.hapi.fhir</groupId>
+          <artifactId>org.hl7.fhir.dstu3</artifactId>
+        </exclusion>
+        <exclusion>
+          <groupId>ca.uhn.hapi.fhir</groupId>
+          <artifactId>org.hl7.fhir.dstu2016may</artifactId>
+        </exclusion>
+        <exclusion>
+          <groupId>ca.uhn.hapi.fhir</groupId>
+          <artifactId>hapi-fhir-structures-dstu3</artifactId>
+        </exclusion>
+        <exclusion>
+          <groupId>ca.uhn.hapi.fhir</groupId>
+          <artifactId>hapi-fhir-structures-r5</artifactId>
+        </exclusion>
+      </exclusions>
     </dependency>
     <dependency>
       <groupId>org.opencds.cqf.cql</groupId>
       <artifactId>evaluator.builder</artifactId>
-      <version>${opencds.cql.version}</version>
+      <version>${cql.version}</version>
     </dependency>
     <dependency>
       <groupId>org.opencds.cqf.cql</groupId>
       <artifactId>evaluator.dagger</artifactId>
-      <version>${opencds.cql.version}</version>
+      <version>${cql.version}</version>
     </dependency>
     <dependency>
       <groupId>org.opencds.cqf.cql</groupId>
       <artifactId>evaluator.plandefinition</artifactId>
-      <version>${opencds.cql.version}</version>
+      <version>${cql.version}</version>
     </dependency>
 
     <dependency>
@@ -291,19 +317,29 @@
         </executions>
       </plugin>
       <plugin>
-        <!-- Build an executable JAR -->
         <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-jar-plugin</artifactId>
-        <version>${maven.jar.plugin.version}</version>
-        <configuration>
-          <archive>
-            <manifest>
-              <addClasspath>true</addClasspath>
-              <classpathPrefix>libs/</classpathPrefix>
-              <mainClass>org.smartregister.Main</mainClass>
-            </manifest>
-          </archive>
-        </configuration>
+        <artifactId>maven-assembly-plugin</artifactId>
+        <executions>
+          <execution>
+            <goals>
+              <goal>single</goal>
+            </goals>
+            <phase>package</phase>
+            <configuration>
+              <archive>
+                <manifest>
+                  <mainClass>org.smartregister.Main</mainClass>
+                </manifest>
+              </archive>
+              <descriptors>
+                <descriptor>src/main/resources/dependency-set.xml</descriptor>
+              </descriptors>
+              <descriptorRefs>
+                <descriptorRef>jar-with-dependencies</descriptorRef>
+              </descriptorRefs>
+            </configuration>
+          </execution>
+        </executions>
       </plugin>
 
     </plugins>

src/main/java/org/smartregister/Main.java

@@ -11,15 +11,15 @@
 @Command(
     name = "fct",
     description = "FHIRCore tooling to make content authoring easier.",
-    version = "1.0.0",
+    version = "2.0.0",
     mixinStandardHelpOptions = true,
     subcommands = {
       ConvertCommand.class,
       StructureMapExtractResourcesCommand.class,
       ValidateCommand.class
     })
 public class Main implements Runnable {
-  public static final String VERSION = "1.0.0";
+  public static final String VERSION = "2.0.0";
 
   @CommandLine.Option(
       names = {"-v"},

src/main/java/org/smartregister/command/ValidateCommand.java

@@ -24,17 +24,53 @@ public class ValidateCommand implements Runnable {
       required = true)
   private String compositionFilePath;
 
+  @CommandLine.Option(
+      names = {"-sm", "--structure-maps"},
+      description =
+          "directory path to the location of structure map .txt or .map files. Must be a directory. Must be used with the -q flag",
+      required = false)
+  private String structureMapsFolderPath;
+
+  @CommandLine.Option(
+      names = {"-q", "--questionnaires"},
+      description =
+          "directory path to the location of questionnaires .json files. Must be a directory. Must be used with the -sm flag",
+      required = false)
+  private String questionnairesFolderPath;
+
   @Override
   public void run() {
 
     if (!Files.isDirectory(Paths.get(inputFolder))) {
-      throw new RuntimeException("path needs to be a directory");
+      throw new RuntimeException("-i, --input configs input path needs to be a directory");
+    }
+
+    if (structureMapsFolderPath != null && questionnairesFolderPath == null) {
+
+      throw new RuntimeException(
+          "You have supplied a -sm, --structure-maps flag without a corresponding -q, --questionnaires flag");
+
+    } else if (structureMapsFolderPath == null && questionnairesFolderPath != null) {
+      throw new RuntimeException(
+          "You have supplied a -q, --questionnaires flag without a corresponding -sm, --structure-maps flag");
+    }
+
+    if (structureMapsFolderPath != null) {
+
+      if (!Files.isDirectory(Paths.get(structureMapsFolderPath))) {
+        throw new RuntimeException("-sm, --structure-maps path needs to be a directory");
+      }
+
+      if (!Files.isDirectory(Paths.get(questionnairesFolderPath))) {
+        throw new RuntimeException("-q, --questionnaires path needs to be a directory");
+      }
     }
 
     try {
 
       FCTValidationEngine FCTValidationEngine = new FCTValidationEngine();
-      FCTValidationEngine.process(compositionFilePath, inputFolder);
+      FCTValidationEngine.process(
+          compositionFilePath, structureMapsFolderPath, questionnairesFolderPath, inputFolder);
 
     } catch (IOException e) {
       logger.severe(e.getMessage());

src/main/java/org/smartregister/util/FCTUtils.java

@@ -12,9 +12,10 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.nio.charset.StandardCharsets;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
+import java.nio.file.*;
+import java.nio.file.attribute.BasicFileAttributes;
+import java.util.HashMap;
+import java.util.Map;
 import java.util.Properties;
 import org.smartregister.domain.FCTFile;
 
@@ -123,6 +124,31 @@ public static void printCompletedInDuration(long startTime) {
             FCTUtils.getHumanDuration(System.currentTimeMillis() - startTime)));
   }
 
+  public static Map<String, Map<String, String>> indexConfigurationFiles(String inputDirectoryPath)
+      throws IOException {
+    Map<String, Map<String, String>> filesMap = new HashMap<>();
+    Path rootDir = Paths.get(inputDirectoryPath);
+    Files.walkFileTree(
+        rootDir,
+        new SimpleFileVisitor<>() {
+          @Override
+          public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) {
+            if (!Files.isDirectory(file)) {
+
+              String parentDirKey =
+                  file.getParent().equals(rootDir)
+                      ? FCTValidationEngine.Constants.ROOT
+                      : file.getParent().getFileName().toString();
+              Map<String, String> fileList = filesMap.getOrDefault(parentDirKey, new HashMap<>());
+              fileList.put(file.getFileName().toString(), file.toAbsolutePath().toString());
+              filesMap.put(parentDirKey, fileList);
+            }
+            return FileVisitResult.CONTINUE;
+          }
+        });
+    return filesMap;
+  }
+
   public static final class Constants {
     public static final String HL7_FHIR_PACKAGE = "hl7.fhir.r4.core";
     public static final String HL7_FHIR_PACKAGE_VERSION = "4.0.1";