Merging tEMinatoRs into the starting super-femr branch

.circleci/config.yml

@@ -18,6 +18,7 @@ jobs:
                     apt-get update
                     apt-get install -y python-pip git
                     pip install awscli
+                    pip install argostranslate
                     apt-get clean && apt-get autoclean
       - checkout
       - restore_cache:
@@ -52,6 +53,7 @@ jobs:
                     apt-get update
                     apt-get install -y python-pip git
                     pip install awscli
+                    pip install argostranslate
                     apt-get clean && apt-get autoclean
       - checkout
       - restore_cache:

.github/workflows/license_check.yml

@@ -0,0 +1,18 @@
+name: Check for LICENSE File in femr Directory
+
+on:
+  push:
+
+jobs:
+  check-license-file:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Check if file exists
+        run: |
+          if [ ! -f "./LICENSE" ]; then
+            echo "File does not exist. Exiting with failure."
+            exit 1
+          fi

.gitignore

@@ -71,3 +71,10 @@ util/PhotoMigration.class
 
 #development database
 docker-compose.yml
+
+speedtest/__pycache__
+
+#Translation Models and Log
+translator/argos_models
+translator/marian_models
+translator/__pycache__

Build.sbt

@@ -16,11 +16,12 @@ val appDependencies = Seq(
   evolutions,
   jodaForms,
   guice,
+  "org.json" % "json" % "20240303",
   "mysql" % "mysql-connector-java" % "5.1.49",
   "org.mindrot" % "jbcrypt" % "0.3m",
   "org.apache.commons" % "commons-collections4" % "4.0",
   "org.apache.commons" % "commons-text" % "1.3",
-  "org.mockito" % "mockito-core" % "3.5.13",
+  "org.mockito" % "mockito-inline" % "3.5.13",
   "com.google.code.gson" % "gson" % "2.3.1",
   "com.itextpdf" % "itextpdf" % "5.5.6",
   "com.itextpdf.tool" % "xmlworker" % "5.5.6",

Dockerfile

@@ -24,7 +24,8 @@ RUN mkdir -p $PROJECT_HOME/activator $PROJECT_HOME/app
 WORKDIR $PROJECT_WORKPLACE/activator
 
 # Install Play Framework
-RUN curl -O http://downloads.typesafe.com/typesafe-activator/1.3.6/typesafe-activator-1.3.6.zip 
+RUN curl -O https://downloads.typesafe.com/typesafe-activator/1.3.6/typesafe-activator-1.3.6.zip
+
 RUN unzip typesafe-activator-1.3.6.zip -d / && rm typesafe-activator-1.3.6.zip && ls && sudo chmod a+x /activator-dist-1.3.6/activator
 ENV PATH $PATH:/activator-1.3.6
 
@@ -35,11 +36,16 @@ RUN \
 
 # Install sbt
 RUN \
-  curl -L -o sbt-$SBT_VERSION.deb https://dl.bintray.com/sbt/debian/sbt-$SBT_VERSION.deb && \
+  mkdir /working/ && \
+  cd /working/ && \
+  curl -L -o sbt-$SBT_VERSION.deb https://repo.scala-sbt.org/scalasbt/debian/sbt-$SBT_VERSION.deb && \
   dpkg -i sbt-$SBT_VERSION.deb && \
   rm sbt-$SBT_VERSION.deb && \
   apt-get update && \
-  apt-get install sbt
+  apt-get install sbt && \
+  cd && \
+  rm -r /working/ && \
+  sbt sbtVersion
 
 # Setup path variables and copy fEMR into container
 ENV PATH $PROJECT_HOME/activator/activator-dist-1.3.10/bin:$PATH

README.md

@@ -1,4 +1,4 @@
-# FEMR - Fast Electronic Medical Records
+# tEMR - Dynamic Translation for FEMR
 
 ![Build Status](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiMVBXNWNSMnZsYkgxb05IYS9rclF4eE9QcVdZT1JBNWI1V3RucFd1cXd4ZVEzTzZ5ZWREaEJJRXRDbExyY243eG05VVV4cWVkQXlMelN1bnkxY2dHUUlZPSIsIml2UGFyYW1ldGVyU3BlYyI6IjlCTnI2U0hvU00yNjROQnQiLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=master)
 
@@ -8,15 +8,25 @@
 
 fEMR is a fast EMR solution for remote clinics who depend on speed and ease of use rather than complex features. Check out [Team fEMR's website](https://teamfemr.org) for more information and a live demo.
 
+### tEMR Dynamic Translation
+
+tEMR is working on a dynamic translation service for physicians and healthcare coders who may write and read in different languages but must be on the same page. Our dynamic translation involves neural networks like Argos (OpenNMT) working in the background in python.
+
 ### Community
 1. [Slack](http://teamfemr.org/slack.html)
 2. [JIRA](https://teamfemr.atlassian.net)
 3. [Team FEMR](https://teamfemr.org)
 
+### tEMR Community
+1. [JIRA](https://platinum.cscaws.com:8443/projects/TEMR/summary)
+
 ### Dependencies
 
 * [Play Framework](http://www.playframework.com/)
 
+### Technical Specification
+For further specification of tEMR contributions, please see the tEMRTechSpec.pdf file.
+
 ### Contributing
 For more information on contributing, please see the CONTRIBUTING.md file. For details regarding installation and deployment, continue reading.
 
@@ -65,16 +75,17 @@ Email: [email protected]
 - `git checkout super-femr`
 
 ### Step 3: Setting up the DB 
-1. Open the MySQL Workbench.
-2. Select the db icon to create a new schema and call it `femr_db`.
+1. Make sure your MySQL server is running on your machine.
+2. Open the MySQL Workbench.
+3. Select the db icon to create a new schema and call it `femr_db`.
 
 <details> <summary> screenshot </summary>
 
 ![Image](https://github.com/kylene-phillips/femr-installation/blob/gh-pages/images/mysqlworkbench1.png?raw=true)
 
 </details>
 
-3. Under the Administration tab, select `User and Priviliges`. Then `Add account` and add `Login name` and `Password` of your preference. Save the login and password because you will need it in the later steps. 
+4. Under the Administration tab, select `User and Priviliges`. Then `Add account` and add `Login name` and `Password` of your preference. Save the login and password because you will need it in the later steps. 
      - For this example, the username is `testing` and password is `password`.
 
 <details> <summary> screenshot </summary>
@@ -83,7 +94,7 @@ Email: [email protected]
 
 </details>
 
-4. Then go to the `Schema Privileges` tab, select `Add Entry...` for the user you created in the previous step, and select the `femr_db` schema.
+5. Then go to the `Schema Privileges` tab, select `Add Entry...` for the user you created in the previous step, and select the `femr_db` schema.
 
 <details> <summary> screenshot </summary>
 
@@ -93,7 +104,7 @@ Email: [email protected]
 
 </details>
 
-5. Give all of the rights, except the `GRANT OPTION`. 
+6. Give all of the rights, except the `GRANT OPTION`. 
 
 <details> <summary> screenshot </summary>
 
@@ -113,14 +124,15 @@ Email: [email protected]
 ```
 include "application.conf"
 settings.researchOnly=0
-db.default.url="jdbc:mysql://127.0.0.1:3306/femr_db?characterEncoding=UTF-8"
+db.default.url="jdbc:mysql://127.0.0.1:3306/femr_db?characterEncoding=UTF-8&useSSL=false"
 db.default.username="testing"
 db.default.password="password"
 photos.defaultProfilePhoto="./public/img/defaultProfile.png"
 csv.path="./Upload/CSV"
 ```
 
 5. Go to `Run` -> `Edit Configurations` -> click on the `+` sign -> `Play 2 App`.
+   - If `Play 2 App` doesn't appear, try restarting the IDE.
 
 <details> <summary> screenshot </summary>
 

app/femr/business/helpers/QueryProvider.java

@@ -166,4 +166,6 @@ public static Query<ResearchEncounterVital> getResearchEncounterVitalQuery() {
     public static Query<InternetStatus> getInternetStatusQuery() {
         return Ebean.find(InternetStatus.class);
     }
+
+    public static Query<LanguageCode> getLanguage() {return Ebean.find(LanguageCode.class);}
 }

app/femr/business/services/core/IUpdatesService.java

@@ -20,9 +20,11 @@
 
 import femr.common.dtos.ServiceResponse;
 import femr.data.models.core.IKitStatus;
+import femr.data.models.core.ILanguageCode;
 import femr.data.models.core.INetworkStatus;
 import femr.data.models.core.IDatabaseStatus;
 
+import java.util.ArrayList;
 import java.util.List;
 
 public interface IUpdatesService {
@@ -68,4 +70,11 @@ public interface IUpdatesService {
      * @return a list of kit database status.
      */
     ServiceResponse<List<? extends IDatabaseStatus>> updateDatabaseStatuses();
+
+    ServiceResponse<List<? extends ILanguageCode>> retrieveLanguages();
+    ServiceResponse<List<? extends ILanguageCode>> initializeLanguages();
+
+    ServiceResponse<List<? extends ILanguageCode>> downloadPackages(String langCode);
+
+    ServiceResponse<List<? extends ILanguageCode>> updateLanguage(String code, boolean updateScheduled);
 }

app/femr/business/services/system/EncounterService.java

@@ -18,12 +18,15 @@
 */
 package femr.business.services.system;
 
+import femr.business.services.core.ISessionService;
+import femr.common.dtos.CurrentUser;
 import io.ebean.ExpressionList;
 import io.ebean.Query;
 import com.google.inject.Inject;
 import com.google.inject.name.Named;
 import femr.business.helpers.QueryProvider;
 import femr.business.services.core.IEncounterService;
+import femr.business.services.core.ISessionService;
 import femr.common.IItemModelMapper;
 import femr.common.dtos.ServiceResponse;
 import femr.common.models.*;
@@ -46,6 +49,7 @@ public class EncounterService implements IEncounterService {
     private final IRepository<IChiefComplaint> chiefComplaintRepository;
     private final IPatientRepository patientRepository;
     private final IEncounterRepository patientEncounterRepository;
+    private final ISessionService sessionService;
     private final IRepository<IPatientEncounterTabField> patientEncounterTabFieldRepository;
     private final IRepository<ITabField> tabFieldRepository;
     private final IUserRepository userRepository;
@@ -56,6 +60,7 @@ public class EncounterService implements IEncounterService {
     public EncounterService(IRepository<IChiefComplaint> chiefComplaintRepository,
                             IPatientRepository patientRepository,
                             IEncounterRepository patientEncounterRepository,
+                            ISessionService sessionService,
                             IRepository<IPatientEncounterTabField> patientEncounterTabFieldRepository,
                             IRepository<ITabField> tabFieldRepository,
                             IUserRepository userRepository,
@@ -65,6 +70,7 @@ public EncounterService(IRepository<IChiefComplaint> chiefComplaintRepository,
         this.chiefComplaintRepository = chiefComplaintRepository;
         this.patientRepository = patientRepository;
         this.patientEncounterRepository = patientEncounterRepository;
+        this.sessionService = sessionService;
         this.patientEncounterTabFieldRepository = patientEncounterTabFieldRepository;
         this.tabFieldRepository = tabFieldRepository;
         this.userRepository = userRepository;
@@ -77,7 +83,7 @@ public EncounterService(IRepository<IChiefComplaint> chiefComplaintRepository,
      */
     @Override
     public ServiceResponse<PatientEncounterItem> createPatientEncounter(int patientId, int userId, Integer tripId, String ageClassification, List<String> chiefComplaints) {
-
+        System.out.println("Create Patient Encounter");
         ServiceResponse<PatientEncounterItem> response = new ServiceResponse<>();
 
         try {
@@ -98,8 +104,9 @@ public ServiceResponse<PatientEncounterItem> createPatientEncounter(int patientI
             if (patientAgeClassification != null)
                 patientAgeClassificationId = patientAgeClassification.getId();
 
-            IPatientEncounter newPatientEncounter = patientEncounterRepository.createPatientEncounter(patientId, dateUtils.getCurrentDateTime(), nurseUser.getId(), patientAgeClassificationId, tripId);
-
+            CurrentUser currentUserSession = sessionService.retrieveCurrentUserSession();
+            String languageCode = currentUserSession.getLanguageCode();
+            IPatientEncounter newPatientEncounter = patientEncounterRepository.createPatientEncounter(patientId, dateUtils.getCurrentDateTime(), nurseUser.getId(), patientAgeClassificationId, tripId, languageCode);
             List<IChiefComplaint> chiefComplaintBeans = new ArrayList<>();
             Integer chiefComplaintSortOrder = 0;
             for (String cc : chiefComplaints) {

app/femr/business/services/system/PatientService.java

@@ -123,7 +123,8 @@ public ServiceResponse<PatientItem> updatePatientPhoneNumber(int id, String phon
                         null,
                         null,
                         null,
-                        null);
+                        null
+                        );
                 //Osman
 
                 response.setResponseObject(patientItem);
@@ -304,7 +305,8 @@ public ServiceResponse<PatientItem> updatePatientAddress(int id, String address)
                         null,
                         null,
                         null,
-                        null);
+                        null
+                        );
                 //Osman
                 response.setResponseObject(patientItem);
             }

app/femr/business/services/system/SessionService.java

@@ -155,7 +155,8 @@ public void invalidateCurrentUserSession() {
     private CurrentUser createCurrentUser(IUser user, Integer tripId) {
 
         long timeout = Long.valueOf(configuration.getString("sessionTimeout")) * 1000 * 60;
-        return new CurrentUser(user.getId(), user.getFirstName(), user.getLastName(), user.getEmail(), user.getRoles(), tripId, timeout);
+        return new CurrentUser(user.getId(), user.getFirstName(), user.getLastName(),
+                user.getEmail(), user.getRoles(), tripId, timeout, user.getLanguageCode());
     }
 }