Added handling of different environments for speedtest.py call in adm…

…in/updates (#747)

* Triage image upload now uploads image properly for patient profile photo

* updated iPhotoService javadoc

* Fixed update page, refresh internet status still broken

* python script needs to be ran first, working on it

* internet update button works admin/updates

* Merged Kevin's changes

* Changed scala file

* Added compatibility for running refresh internet status in docker and IDE

.circleci/config.yml

@@ -18,6 +18,7 @@ jobs:
                     apt-get update
                     apt-get install -y python-pip git
                     pip install awscli
+                    pip install psutil
                     pip install argostranslate
                     apt-get clean && apt-get autoclean
       - checkout
@@ -54,6 +55,7 @@ jobs:
                     apt-get install -y python-pip git
                     pip install awscli
                     pip install argostranslate
+                    pip install psutil
                     apt-get clean && apt-get autoclean
       - checkout
       - restore_cache:

Dockerfile

@@ -1,66 +1,84 @@
-FROM ubuntu
-
-RUN apt-get update -y
-RUN apt-get install -y sudo
-
-#get java
-RUN sudo apt install -y openjdk-8-jdk
-
-RUN sudo apt-get install -y wget
-RUN sudo apt-get install -y unzip
-RUN sudo apt-get install -y curl
+FROM sbtscala/scala-sbt:eclipse-temurin-jammy-8u352-b08_1.9.0_2.12.17 AS builder
 
 #build varaibles
-ENV SBT_VERSION 1.1.5
+#ENV SBT_VERSION 1.1.5
 ENV PROJECT_HOME /usr/src
 
-#database variables
-ENV DB_URL "jdbc:mysql://localhost:3306/femr_db?characterEncoding=UTF-8&useSSL=false"
-ENV DB_USER "username"
-ENV DB_PASS "password"
+#RUN mkdir -p $PROJECT_HOME/activator $PROJECT_HOME/app
 
-RUN mkdir -p $PROJECT_HOME/activator $PROJECT_HOME/app
+RUN apt-get update && apt-get install -y \
+    unzip \
+    && rm -rf /var/lib/apt/lists/*
 
-WORKDIR $PROJECT_WORKPLACE/activator
+#WORKDIR $PROJECT_WORKPLACE/activator
+#RUN wget https://downloads.typesafe.com/typesafe-activator/1.3.6/typesafe-activator-1.3.6.zip && \
+#    unzip typesafe-activator-1.3.6.zip && chmod a+x activator-dist-1.3.6/activator
+#ENV PATH $PATH:/activator-1.3.6
 
 # Install Play Framework
-RUN curl -O https://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
+#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
 
 # Install curl
-RUN \
-  apt-get update && \
-  apt-get -y install curl
+#RUN \
+ # apt-get update && \
+ # apt-get -y install curl
 
 # Install sbt
-RUN \
-  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 && \
-  cd && \
-  rm -r /working/ && \
-  sbt sbtVersion
+#RUN \
+  #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 && \
+  #cd && \
+  #rm -r /working/ && \
+  #sbt sbtVersion
+
+COPY Build.sbt .
+COPY project ./project
+
+RUN --mount=type=cache,target=/root/.ivy2 \
+        --mount=type=cache,target=/root/.sbt \
+        sbt update
 
 # Setup path variables and copy fEMR into container
-ENV PATH $PROJECT_HOME/activator/activator-dist-1.3.10/bin:$PATH
-ENV PATH $PROJECT_WORKPLACE/build/target/universal/stage/bin:$PATH
+#ENV PATH $PROJECT_HOME/activator/activator-dist-1.3.10/bin:$PATH
+#ENV PATH $PROJECT_WORKPLACE/build/target/universal/stage/bin:$PATH
 COPY . $PROJECT_HOME/app
+COPY ../speedtest /usr/src/speedtest
 WORKDIR $PROJECT_HOME/app
 
 RUN \
     rm $PROJECT_HOME/app/conf/application.conf && \
     mv $PROJECT_HOME/app/conf/application.docker.conf $PROJECT_HOME/app/conf/application.conf
 
-RUN sbt clean compile
+#RUN sbt clean compile
+RUN --mount=type=cache,target=/root/.ivy2 \
+    --mount=type=cache,target=/root/.sbt \
+    sbt dist
+
+WORKDIR $PROJECT_HOME/app/target/universal
+RUN unzip femr-*.zip && rm femr-*.zip
+
+FROM openjdk:jre-alpine
+
+RUN apk add --no-cache bash python3 py3-pip gcc python3-dev musl-dev linux-headers
+RUN pip3 install psutil
+
+#database variables
+ENV DB_URL "jdbc:mysql://localhost:3306/femr_db?characterEncoding=UTF-8&useSSL=false"
+ENV DB_USER "username"
+ENV DB_PASS "password"
+
+COPY --from=builder /usr/src/app/target/universal/femr-* /opt/bin/femr
 
 #open port 9000 for connections
 EXPOSE 9000
 
 # run fEMR using env variables
-ENTRYPOINT url=$DB_URL usr=$DB_USER pass=$DB_PASS sbt ~run
+#ENTRYPOINT url=$DB_URL usr=$DB_USER pass=$DB_PASS sbt ~run
+ENTRYPOINT ["/bin/bash", "-c", "/opt/bin/femr/bin/femr"]

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

@@ -35,6 +35,8 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.security.UnresolvedPermission;
 import java.util.ArrayList;
 import java.util.List;
@@ -83,7 +85,15 @@ public  ServiceResponse<List<? extends INetworkStatus>> updateNetworkStatuses()
         ServiceResponse<List<? extends INetworkStatus>> response = new ServiceResponse<>();
         ArrayList<String> data = new ArrayList<>();
         try {
-            data = BackEndControllerHelper.executeSpeedTestScript("speedtest/sptest.py");
+            String isDocker = System.getenv("IS_DOCKER");
+            if("true".equals(isDocker)) { //running in docker
+                data = BackEndControllerHelper.executeSpeedTestScript("/usr/src/speedtest/sptest.py");
+            }else{ //running in IDE
+                Path speedPath = Paths.get(System.getProperty("user.dir"), "speedtest", "sptest.py");
+                data = BackEndControllerHelper.executeSpeedTestScript(speedPath.toString());
+            }
+            //data = BackEndControllerHelper.executeSpeedTestScript("/usr/src/speedtest/sptest.py");
+            //data = BackEndControllerHelper.executeSpeedTestScript("speedtest/sptest.py");
             //Update Status
             Float Ping = Float.parseFloat(data.get(2));
             String updatedStatus = "Connection stable";

app/femr/common/dtos/ServiceResponse.java

@@ -34,7 +34,7 @@ public ServiceResponse() {
     }
 
     public boolean hasErrors() {
-        return errors.size() > 0;
+        return !errors.isEmpty();
     }
 
     public T getResponseObject() {

app/femr/data/DataModelMapper.java

@@ -451,6 +451,7 @@ public IPhoto createPhoto(String description, String filePath, byte[] photoData)
         if (StringUtils.isNullOrWhiteSpace(description)) photo.setDescription("");
         else photo.setDescription(description);
         photo.setFilePath(filePath);
+        photo.setInsertTS(new Date());
 
         if(photoData != null)
             photo.setPhotoBlob(photoData);

app/femr/ui/controllers/BackEndControllerHelper.java

@@ -23,7 +23,12 @@ public static void executePythonScript(String absPath) {
   public static ArrayList<String> executeSpeedTestScript(String absPath) {
     ArrayList<String> speedInfo = new ArrayList<>();
     try {
-      ProcessBuilder pb = new ProcessBuilder("python", absPath);
+      ProcessBuilder pb;
+      if(absPath.equals("/usr/src/speedtest/sptest.py")){
+        pb = new ProcessBuilder("python3", absPath);
+      }else{
+        pb = new ProcessBuilder("python", absPath);
+      }
       Process p = pb.start();
       BufferedReader bfr = new BufferedReader(new InputStreamReader(p.getInputStream(), "UTF-8"));
 

app/femr/ui/controllers/admin/UpdatesController.java

@@ -75,6 +75,8 @@ public Result manageGet() {
         if (networkStatusesResponse.hasErrors()) {
             throw new RuntimeException();
         }
+
+
         for (INetworkStatus ns : networkStatusesResponse.getResponseObject()) {
             indexViewModel.setNetworkStatus(ns.getName(), ns.getValue());
         }
@@ -83,6 +85,8 @@ public Result manageGet() {
         if (kitStatusesResponse.hasErrors()) {
             throw new RuntimeException();
         }
+
+
         for (IKitStatus ks : kitStatusesResponse.getResponseObject()) {
             indexViewModel.setKitStatus(ks.getName(), ks.getValue());
         }
@@ -91,6 +95,8 @@ public Result manageGet() {
         if (databaseStatusResponse.hasErrors()) {
             throw new RuntimeException();
         }
+
+
         for (IDatabaseStatus ds : databaseStatusResponse.getResponseObject()) {
             indexViewModel.setDatabaseStatus(ds.getName(), ds.getValue());
         }
@@ -101,6 +107,7 @@ public Result manageGet() {
         if(languagesResponse.hasErrors()){
             throw new RuntimeException();
         }
+
         for(ILanguageCode lang : languagesResponse.getResponseObject()) {
             indexViewModel.setLanguages(lang);
         }
@@ -140,6 +147,7 @@ public Result kitUpdatePost() {
 
         return manageGet();
     }
+
     public Result refreshInternetStatus() {
         ServiceResponse<List<? extends INetworkStatus>> updateResponse = updatesService.updateNetworkStatuses();
         if (updateResponse.hasErrors()) {
@@ -151,6 +159,7 @@ public Result refreshInternetStatus() {
     }
 
     public Result updateLanguage(){
+
         String langCode = request().getQueryString("code");
         boolean updateScheduled = request().getQueryString("update").equals("true");
 

app/femr/ui/views/admin/updates/manage.scala.html

@@ -9,12 +9,16 @@
     @additionalStyles = {
         <link rel="stylesheet" href="@assets.path("css/admin/configure.css")">
     }
+
     @additionalMessages = {
+
         @for(message <- messages) {
-        <p class="adminMessage">@message</p>
+            <p class="adminMessage">@message</p>
         }
+
     }
-    @downloadSpeed = @{viewModel.getNetworkStatus.get("Download").substring(0, viewModel.getNetworkStatus.get("Download").indexOf(".")).toInt}
+
+@downloadSpeed = @{ viewModel.getNetworkStatus.get("Download").split(" ")(0).toFloat.toInt }
 
 @admin("Updates", currentUser, styles = additionalStyles, assets = assets, message = additionalMessages) {
 
@@ -23,7 +27,7 @@
                 <div id="network-status">
                     <h2>Network Status</h2>
 
-                    <table id="networkstatus">`
+                    <table id="networkstatus">
                         <div>
                             <div>
                             @helper.form(action = UpdatesController.refreshInternetStatus()) {
@@ -42,7 +46,7 @@ <h2>Network Status</h2>
                                 }
                             </div>
                         </div>
-                        @for((key,valyew) <- viewModel.getNetworkStatus) {
+                         @for((key,valyew) <- viewModel.getNetworkStatus) {
                             <tr>
                                 <td>@key:</td>
                                 <td>@valyew</td>
@@ -88,6 +92,7 @@ <h2>Languages</h2>
                 </div>
             </div>
 
+
             <div id="right-div">
                 <div id="language-package-updates">
                     <h2>Scheduled Languages</h2>
@@ -132,7 +137,7 @@ <h2>Database Status</h2>
                     <h2>Available Updates</h2>
                     <table>
                         <tr>
-                        @if(viewModel.isUpdateAvailable) {
+                         @if(viewModel.isUpdateAvailable) {
                             @helper.form(action = UpdatesController.kitUpdatePost()) {
                                 <td>Kit Update: Available</td><td>
                                     <input type="submit" class="fButton" value="Update"/></td>
@@ -145,4 +150,5 @@ <h2>Available Updates</h2>
                 </div>
             </div>
         </div>
+
 }

conf/application.docker.conf

@@ -21,9 +21,9 @@ play.il8n.langs="en"
 
 #Register MySQL database settings
 db.default.driver="com.mysql.jdbc.Driver"
-db.default.url=${?url}
-db.default.username=${?usr}
-db.default.password=${?pass}
+db.default.url=${?DB_URL}
+db.default.username=${?DB_USER}
+db.default.password=${?DB_PASS}
 db.default.logStatements=false
 
 #Register paths for photos

conf/logback.xml

@@ -34,7 +34,7 @@
   <logger name="play" level="INFO" />
   <logger name="application" level="DEBUG" />
 
-  <root level="WARN">
+  <root level="INFO">
     <appender-ref ref="ASYNCFILE" />
     <appender-ref ref="ASYNCSTDOUT" />
   </root>

docker-compose.yml

@@ -28,15 +28,15 @@ services:
     tty: true
     ports:
       - '9000:9000'
-    expose:
-      - '9000'
-    volumes:
-      - ./femr/conf:/home/femrapp/conf
+
     environment:
       DB_URL: 'jdbc:mysql://db:3306/femr_db?characterEncoding=UTF-8&useSSL=false&allowPublicKeyRetrieval=true'
       DB_USER: 'femr'
       DB_PASS: 'password'
+      IS_DOCKER: 'true'
 
+    volumes:
+      - ./speedtest:/usr/src/speedtest
 
 
 volumes: