Merge pull request #227 from DBCG/develop

0.3.0 Release
cqframework · Jul 8, 2020 · a3166f0 · a3166f0
2 parents ed186b8 + ea5ebca
commit a3166f0
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Showing 128 changed files with 4,115 additions and 3,138 deletions.
diff --git a/.dockerignore b/.dockerignore
@@ -5,5 +5,4 @@
 .project
 examples
 target
-derby.log
-!target/jpaserver_derby_files
+derby.log
diff --git a/.gitignore b/.gitignore
@@ -156,10 +156,10 @@ org.eclipse.m2e.core.prefs
 LogMessages.html
 
 *.zip
+*.7z
 
 core.*
 heapdump.*
 Snap.*
 
-.flattened-pom.xml
-
+.flattened-pom.xml
diff --git a/common/src/main/java/org/opencds/cqf/common/config/FhirServerConfig.java b/common/src/main/java/org/opencds/cqf/common/config/FhirServerConfig.java
@@ -3,15 +3,14 @@
 import java.lang.reflect.InvocationTargetException;
 import java.sql.Driver;
 
-import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import org.apache.commons.dbcp2.BasicDataSource;
 import org.springframework.beans.factory.annotation.Autowire;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
 import ca.uhn.fhir.jpa.dao.DaoConfig;
-import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
+import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.rest.server.interceptor.LoggingInterceptor;
 import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
 
@@ -35,7 +34,8 @@ public FhirServerConfig() {
         ourLog.info("Server configured to " + (this.allowExternalReferences ? "allow" : "deny") + " external references");
         ourLog.info("Server configured to " + (this.expungeEnabled ? "enable" : "disable") + " expunges");
         ourLog.info("Server configured to " + (this.allowPlaceholderReferences ? "allow" : "deny") + " placeholder references");
-        ourLog.info("Server configured to " + (this.allowOverrideDefaultSearchParams ? "allow" : "deny") + " overriding default search params");
+        ourLog.info("Server configured to " + (this.allowOverrideDefaultSearchParams ? "allow" : "deny")
+                + " overriding default search params");
     }
 
     /**
@@ -54,10 +54,11 @@ public DaoConfig daoConfig() {
 
         Integer maxFetchSize = HapiProperties.getMaximumFetchSize();
         retVal.setFetchSizeDefaultMaximum(maxFetchSize);
-        ourLog.info("Server configured to have a maximum fetch size of " + (maxFetchSize == Integer.MAX_VALUE? "'unlimited'": maxFetchSize));
+        ourLog.info("Server configured to have a maximum fetch size of "
+                + (maxFetchSize == Integer.MAX_VALUE ? "'unlimited'" : maxFetchSize));
 
         Long reuseCachedSearchResultsMillis = HapiProperties.getReuseCachedSearchResultsMillis();
-        retVal.setReuseCachedSearchResultsForMillis(reuseCachedSearchResultsMillis );
+        retVal.setReuseCachedSearchResultsForMillis(reuseCachedSearchResultsMillis);
         ourLog.info("Server configured to cache search results for {} milliseconds", reuseCachedSearchResultsMillis);
 
         return retVal;
@@ -75,16 +76,17 @@ public ModelConfig modelConfig() {
     }
 
     /**
-     * The following bean configures the database connection. The 'url' property value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates that the server should save resources in a
-     * directory called "jpaserver_derby_files".
+     * The following bean configures the database connection. The 'url' property
+     * value of "jdbc:derby:directory:jpaserver_derby_files;create=true" indicates
+     * that the server should save resources in a directory called
+     * "jpaserver_derby_files".
      *
-     * A URL to a remote database could also be placed here, along with login credentials and other properties supported by BasicDataSource.
+     * A URL to a remote database could also be placed here, along with login
+     * credentials and other properties supported by BasicDataSource.
      */
     @Bean(destroyMethod = "close")
-    public BasicDataSource dataSource()
-            throws ClassNotFoundException, NoSuchMethodException, IllegalAccessException,
-            InvocationTargetException, InstantiationException
-    {
+    public BasicDataSource dataSource() throws ClassNotFoundException, NoSuchMethodException, IllegalAccessException,
+            InvocationTargetException, InstantiationException {
         BasicDataSource retVal = new BasicDataSource();
         Driver driver = (Driver) Class.forName(HapiProperties.getDataSourceDriver()).getConstructor().newInstance();
         retVal.setDriver(driver);
@@ -95,9 +97,9 @@ public BasicDataSource dataSource()
         return retVal;
     }
 
-
     /**
-     * Do some fancy logging to create a nice access log that has details about each incoming request.
+     * Do some fancy logging to create a nice access log that has details about each
+     * incoming request.
      */
     public LoggingInterceptor loggingInterceptor() {
         LoggingInterceptor retVal = new LoggingInterceptor();
@@ -109,7 +111,8 @@ public LoggingInterceptor loggingInterceptor() {
     }
 
     /**
-     * This interceptor adds some pretty syntax highlighting in responses when a browser is detected
+     * This interceptor adds some pretty syntax highlighting in responses when a
+     * browser is detected
      */
     @Bean(autowire = Autowire.BY_TYPE)
     public ResponseHighlighterInterceptor responseHighlighterInterceptor() {

diff --git a/common/src/main/java/org/opencds/cqf/common/config/HapiProperties.java b/common/src/main/java/org/opencds/cqf/common/config/HapiProperties.java
@@ -1,14 +1,15 @@
 package org.opencds.cqf.common.config;
 
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.util.Properties;
+
+import com.google.common.annotations.VisibleForTesting;
+
 import ca.uhn.fhir.context.ConfigurationException;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.server.ETagSupportEnum;
-import com.google.common.annotations.VisibleForTesting;
-
-import java.io.FileInputStream;
-import java.io.InputStream;
-import java.util.Properties;
 
 public class HapiProperties {
     static final String ALLOW_EXTERNAL_REFERENCES = "allow_external_references";
@@ -47,6 +48,21 @@ public class HapiProperties {
     static final String ALLOW_CONTAINS_SEARCHES = "allow_contains_searches";
     static final String ALLOW_OVERRIDE_DEFAULT_SEARCH_PARAMS = "allow_override_default_search_params";
     static final String EMAIL_FROM = "email.from";
+    static final String OAUTH_ENABLED = "oauth.enabled";
+    static final String OAUTH_SECURITY_CORS = "oauth.securityCors";
+    static final String OAUTH_SECURITY_URL = "oauth.securityUrl";
+    static final String OAUTH_SECURITY_EXT_AUTH_URL = "oauth.securityExtAuthUrl";
+    static final String OAUTH_SECURITY_EXT_AUTH_VALUE_URI = "oauth.securityExtAuthValueUri";
+    static final String OAUTH_SECURITY_EXT_TOKEN_URL = "oauth.securityExtTokenUrl";
+    static final String OAUTH_SECURITY_EXT_TOKEN_VALUE_URI = "oauth.securityExtTokenValueUri";
+    static final String OAUTH_SERVICE_SYSTEM = "oauth.serviceSystem";
+    static final String OAUTH_SERVICE_CODE = "oauth.serviceCode";
+    static final String OAUTH_SERVICE_DISPLAY = "oauth.serviceDisplay";
+    static final String OAUTH_SERVICE_TEXT = "oauth.serviceText";
+    static final String QUESTIONNAIRE_RESPONSE_ENABLED = "questionnaireResponseExtract.enabled";
+    static final String QUESTIONNAIRE_RESPONSE_ENDPOINT = "questionnaireResponseExtract.endpoint";
+    static final String QUESTIONNAIRE_RESPONSE_USERNAME = "questionnaireResponseExtract.username";
+    static final String QUESTIONNAIRE_RESPONSE_PASSWORD = "questionnaireResponseExtract.password";
 
     private static Properties properties;
 
@@ -59,8 +75,8 @@ public static void forceReload() {
     }
 
     /**
-     * This is mostly here for unit tests. Use the actual properties file
-     * to set values
+     * This is mostly here for unit tests. Use the actual properties file to set
+     * values
      */
     @VisibleForTesting
     public static void setProperty(String theKey, String theValue) {
@@ -70,39 +86,41 @@ public static void setProperty(String theKey, String theValue) {
     public static Properties getProperties() {
         if (properties == null) {
             // Load the configurable properties file
-            try (InputStream in = HapiProperties.class.getClassLoader().getResourceAsStream(HAPI_PROPERTIES)){
+            try (InputStream in = HapiProperties.class.getClassLoader().getResourceAsStream(HAPI_PROPERTIES)) {
                 HapiProperties.properties = new Properties();
                 HapiProperties.properties.load(in);
             } catch (Exception e) {
                 throw new ConfigurationException("Could not load HAPI properties", e);
             }
 
             Properties overrideProps = loadOverrideProperties();
-            if(overrideProps != null) {
-              properties.putAll(overrideProps);
+            if (overrideProps != null) {
+                properties.putAll(overrideProps);
             }
         }
 
         return properties;
     }
 
     /**
-     * If a configuration file path is explicitly specified via -Dhapi.properties=<path>, the properties there will
-     * be used to override the entries in the default hapi.properties file (currently under WEB-INF/classes)
-     * @return properties loaded from the explicitly specified configuraiton file if there is one, or null otherwise.
+     * If a configuration file path is explicitly specified via
+     * -Dhapi.properties=<path>, the properties there will be used to override the
+     * entries in the default hapi.properties file (currently under WEB-INF/classes)
+     * 
+     * @return properties loaded from the explicitly specified configuraiton file if
+     *         there is one, or null otherwise.
      */
     private static Properties loadOverrideProperties() {
         String confFile = System.getProperty(HAPI_PROPERTIES + "." + HapiProperties.getProperty(FHIR_VERSION));
         if (confFile == null) {
             confFile = System.getProperty(HAPI_PROPERTIES);
         }
-        if(confFile != null) {
+        if (confFile != null) {
             try {
                 Properties props = new Properties();
                 props.load(new FileInputStream(confFile));
                 return props;
-            }
-            catch (Exception e) {
+            } catch (Exception e) {
                 throw new ConfigurationException("Could not load HAPI properties file: " + confFile, e);
             }
         }
@@ -213,7 +231,8 @@ public static String getLoggerName() {
     }
 
     public static String getLoggerFormat() {
-        return HapiProperties.getProperty(LOGGER_FORMAT, "Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]");
+        return HapiProperties.getProperty(LOGGER_FORMAT,
+                "Path[${servletPath}] Source[${requestHeader.x-forwarded-for}] Operation[${operationType} ${operationName} ${idOrResourceName}] UA[${requestHeader.user-agent}] Params[${requestParameters}] ResponseEncoding[${responseEncodingNoDefault}]");
     }
 
     public static String getLoggerErrorFormat() {
@@ -228,16 +247,17 @@ public static String getDataSourceDriver() {
         return HapiProperties.getProperty(DATASOURCE_DRIVER, "org.apache.derby.jdbc.EmbeddedDriver");
     }
 
-    public static Object getDriver() {
-        return new org.apache.derby.jdbc.EmbeddedDriver();
-    }
+    // public static Object getDriver() {
+    //     return new org.apache.derby.jdbc.EmbeddedDriver();
+    // }
 
     public static Integer getDataSourceMaxPoolSize() {
         return HapiProperties.getIntegerProperty(DATASOURCE_MAX_POOL_SIZE, 10);
     }
 
     public static String getDataSourceUrl() {
-        return HapiProperties.getProperty(DATASOURCE_URL, "jdbc:derby:directory:target/jpaserver_derby_files;create=true");
+        return HapiProperties.getProperty(DATASOURCE_URL,
+                "jdbc:derby:directory:target/jpaserver_derby_files;create=true");
     }
 
     public static String getDataSourceUsername() {
@@ -340,4 +360,22 @@ public static Long getReuseCachedSearchResultsMillis() {
         String value = HapiProperties.getProperty(REUSE_CACHED_SEARCH_RESULTS_MILLIS, "-1");
         return Long.valueOf(value);
     }
+
+    //************************* OAuth *******************************************************
+    public static Boolean getOAuthEnabled(){return HapiProperties.getBooleanProperty(OAUTH_ENABLED, false);}
+    public static Boolean getOauthSecurityCors(){return HapiProperties.getBooleanProperty(OAUTH_SECURITY_CORS, true);}
+    public static String getOauthSecurityUrl(){return HapiProperties.getProperty(OAUTH_SECURITY_URL, "");}
+    public static String getOauthSecurityExtAuthUrl(){return HapiProperties.getProperty(OAUTH_SECURITY_EXT_AUTH_URL, "");}
+    public static String getOauthSecurityExtAuthValueUri(){return HapiProperties.getProperty(OAUTH_SECURITY_EXT_AUTH_VALUE_URI, "");}
+    public static String getOauthSecurityExtTokenUrl(){return HapiProperties.getProperty(OAUTH_SECURITY_EXT_TOKEN_URL, "");}
+    public static String getOauthSecurityExtTokenValueUri(){return HapiProperties.getProperty(OAUTH_SECURITY_EXT_TOKEN_VALUE_URI, "");}
+    public static String getOauthServiceSystem(){return HapiProperties.getProperty(OAUTH_SERVICE_SYSTEM, "");}
+    public static String getOauthServiceCode(){return HapiProperties.getProperty(OAUTH_SERVICE_CODE, "");}
+    public static String getOauthServiceDisplay(){return HapiProperties.getProperty(OAUTH_SERVICE_DISPLAY, "");}
+    public static String getOauthServiceText(){return HapiProperties.getProperty(OAUTH_SERVICE_TEXT, "");}
+
+    public static Boolean getQuestionnaireResponseExtractEnabled(){return HapiProperties.getBooleanProperty(QUESTIONNAIRE_RESPONSE_ENABLED, false);}
+    public static String getQuestionnaireResponseExtractEndpoint() {return HapiProperties.getProperty(QUESTIONNAIRE_RESPONSE_ENDPOINT);}
+    public static String getQuestionnaireResponseExtractUserName(){return HapiProperties.getProperty(QUESTIONNAIRE_RESPONSE_USERNAME);};
+    public static String getQuestionnaireResponseExtractPassword(){return HapiProperties.getProperty(QUESTIONNAIRE_RESPONSE_PASSWORD);};
 }
diff --git a/common/src/main/java/org/opencds/cqf/common/evaluation/EvaluationProviderFactory.java b/common/src/main/java/org/opencds/cqf/common/evaluation/EvaluationProviderFactory.java
@@ -1,7 +1,7 @@
 package org.opencds.cqf.common.evaluation;
 
-import org.opencds.cqf.cql.data.DataProvider;
-import org.opencds.cqf.cql.terminology.TerminologyProvider;
+import org.opencds.cqf.cql.engine.data.DataProvider;
+import org.opencds.cqf.cql.engine.terminology.TerminologyProvider;
 
 // TODO: This interface is a partial duplicate of the provider factory interface
 // in the cql service layer. We need another round of refactoring to consolidate that.
@@ -12,5 +12,6 @@ public interface EvaluationProviderFactory {
 
     public DataProvider createDataProvider(String model, String version, TerminologyProvider terminologyProvider);
 
-    public TerminologyProvider createTerminologyProvider(String model, String version, String url, String user, String pass);
+    public TerminologyProvider createTerminologyProvider(String model, String version, String url, String user,
+            String pass);
 }
diff --git a/common/src/main/java/org/opencds/cqf/common/evaluation/LibraryLoader.java b/common/src/main/java/org/opencds/cqf/common/evaluation/LibraryLoader.java
@@ -1,25 +1,27 @@
 package org.opencds.cqf.common.evaluation;
 
-import org.cqframework.cql.cql2elm.CqlTranslator;
-import org.cqframework.cql.cql2elm.CqlTranslatorException;
-import org.cqframework.cql.cql2elm.LibraryManager;
-import org.cqframework.cql.cql2elm.ModelManager;
-import org.cqframework.cql.cql2elm.CqlTranslatorException.ErrorSeverity;
-import org.cqframework.cql.cql2elm.LibraryBuilder.SignatureLevel;
-import org.cqframework.cql.elm.execution.Library;
-import org.cqframework.cql.elm.execution.VersionedIdentifier;
+import static org.opencds.cqf.common.helpers.TranslatorHelper.errorsToString;
+import static org.opencds.cqf.common.helpers.TranslatorHelper.getTranslator;
+import static org.opencds.cqf.common.helpers.TranslatorHelper.readLibrary;
 
-import javax.xml.bind.JAXBException;
 import java.io.ByteArrayInputStream;
 import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.Map;
 
-import static org.opencds.cqf.common.helpers.TranslatorHelper.*;
+import javax.xml.bind.JAXBException;
+
+import org.cqframework.cql.cql2elm.CqlTranslator;
+import org.cqframework.cql.cql2elm.CqlTranslatorException;
+import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
+import org.cqframework.cql.cql2elm.LibraryManager;
+import org.cqframework.cql.cql2elm.ModelManager;
+import org.cqframework.cql.elm.execution.Library;
+import org.cqframework.cql.elm.execution.VersionedIdentifier;
 
-public class LibraryLoader implements org.opencds.cqf.cql.execution.LibraryLoader {
+public class LibraryLoader implements org.opencds.cqf.cql.engine.execution.LibraryLoader {
 
     private LibraryManager libraryManager;
     private ModelManager modelManager;
@@ -78,12 +80,8 @@ private Library loadLibrary(VersionedIdentifier libraryIdentifier) {
                 .withVersion(libraryIdentifier.getVersion());
 
         ArrayList<CqlTranslatorException> errors = new ArrayList<>();
-        org.hl7.elm.r1.Library translatedLibrary = libraryManager.resolveLibrary(identifier, ErrorSeverity.Error,
-                SignatureLevel.All,
-                new CqlTranslator.Options[] { CqlTranslator.Options.EnableAnnotations,
-                        CqlTranslator.Options.EnableLocators, CqlTranslator.Options.DisableListDemotion,
-                        CqlTranslator.Options.DisableListPromotion, CqlTranslator.Options.DisableMethodInvocation },
-                errors).getLibrary();
+        org.hl7.elm.r1.Library translatedLibrary = libraryManager
+                .resolveLibrary(identifier, CqlTranslatorOptions.defaultOptions(), errors).getLibrary();
 
         if (CqlTranslatorException.HasErrors(errors)) {
             throw new IllegalArgumentException(errorsToString(errors));

diff --git a/common/src/main/java/org/opencds/cqf/common/helpers/ClientHelper.java b/common/src/main/java/org/opencds/cqf/common/helpers/ClientHelper.java
@@ -0,0 +1,33 @@
+package org.opencds.cqf.common.helpers;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.rest.client.api.IGenericClient;
+import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
+import ca.uhn.fhir.rest.client.interceptor.BasicAuthInterceptor;
+
+public class ClientHelper {
+
+    /*
+     * TODO - depending on future needs: 1. add OAuth 2. change if to switch to
+     * accommodate additional FHIR versions
+     */
+    private static IGenericClient getRestClient(FhirContext fhirContext, String url) {
+        fhirContext.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
+        return fhirContext.newRestfulGenericClient(url);
+    }
+
+    // Overload in case you need to specify a specific version of the context
+    public static IGenericClient getClient(FhirContext fhirContext, String url, String user, String password) {
+        IGenericClient client = getRestClient(fhirContext, url);
+        registerAuth(client, user, password);
+
+        return client;
+    }
+
+    private static void registerAuth(IGenericClient client, String userId, String password) {
+        if (userId != null) {
+            BasicAuthInterceptor authInterceptor = new BasicAuthInterceptor(userId, password);
+            client.registerInterceptor(authInterceptor);
+        }
+    }
+}