fix snomed import

.github/workflows/linux-docker-build.yml

@@ -33,9 +33,10 @@ jobs:
         docker  build \
           --tag fhirserver \
         .
-    - name: Scan Code
-      run: |
-        docker run --entrypoint /work/fhirserver/utilities/codescan/codescan fhirserver /work/bootstrap
+#    - name: Scan Code
+#      run: |
+#        export DISPLAY=0:0
+#        docker run --entrypoint /work/fhirserver/utilities/codescan/codescan fhirserver /work/bootstrap
     - name: Prepare ini file
       env:
         FHIRSERVER_LOCATIONS_CLONE_PATH: /work/fhirserver
@@ -65,3 +66,15 @@ jobs:
           -v ~/terminology:/terminology \
           -v ~/test-settings.ini:/work/fhirserver/exec/64/test-settings.ini \
           fhirserver -tests
+    -
+      name: Login to Docker Hub
+      uses: docker/login-action@v2
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+    - name: Tag and push Docker image
+      run: |
+        docker tag fhirserver ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:latest
+        docker push ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:latest
+

Dockerfile

@@ -19,10 +19,12 @@ RUN /work/bootstrap/linux-toolchain.sh /work/bootstrap
 WORKDIR /work/fhirserver
 COPY . /work/fhirserver
 
-RUN /work/bootstrap/linux-libraries.sh /work/bootstrap
-RUN cp exec/pack/linux/*.so /usr/lib/
-RUN /work/fhirserver/build/linux-fhirserver.sh /work/bootstrap
-RUN cp exec/pack/*.properties exec/64
+RUN /work/bootstrap/linux-libraries.sh /work/bootstrap && \
+    cp exec/pack/linux/*.so /usr/lib/
+RUN /work/fhirserver/build/linux-fhirserver.sh /work/bootstrap && \
+    cp exec/pack/*.properties exec/64 && \
+    find . -name "*.o" -type f -delete -o -name "*.ppu" -type f -delete
+
 
 ENV DISPLAY :99
 ENV PORT 80
@@ -38,4 +40,4 @@ chmod +x /bin/entrypoint.sh
 
 ENTRYPOINT ["/bin/entrypoint.sh"]
 
-CMD ["-cmd",  "exec",  "-cfg", "http://tx.fhir.org/config", "-version",  "4", "-local", "$TERMINOLOGY_CACHE"]
+CMD ["-cmd",  "exec",  "-cfg", "/config/config.ini", "-local", "$TERMINOLOGY_CACHE"]

config/config.ini

@@ -0,0 +1,6 @@
+[config]
+zero=https://storage.googleapis.com/tx-fhir-org
+version=*
+user=jose
+
+[web]

library/ftx/ftx_loinc_services.pas

@@ -35,7 +35,8 @@
 Uses
   SysUtils, Classes, Generics.Collections, {$IFDEF FPC} LazUTF8,{$ELSE} IOUtils, RegularExpressions, {$ENDIF}
   fsl_base, fsl_utilities, fsl_stream, fsl_collections, fsl_fpc, fsl_lang, fsl_http,
-  fhir_objects, fhir_common, fhir_utilities, fhir_factory, fhir_features, fhir_uris,
+  fhir_objects, fhir_common, fhir_utilities, fhir_factory,
+  fhir_features, fhir_uris,
   fhir_cdshooks,
   ftx_service;
 
@@ -525,6 +526,13 @@ function memU16ToString(const bytes : TBytes; index : cardinal; chars : word) :
 
 // the bytes contain UTF8
 function memU8toString(bytes : TBytes; index, chars : integer) : String;
+{$IFNDEF FPC}
+var
+  utf8str: UTF8String;
+{$ENDIF}
+  var UTFEncoding: TEncoding;
+  theseBytes:TBytes;
+
 begin
   if chars = 0 then
     exit('');
@@ -534,7 +542,13 @@ function memU8toString(bytes : TBytes; index, chars : integer) : String;
   setLength(result, chars);
   Move(bytes[index], result[1], chars);
   {$ELSE}
-  result := TEncoding.UTF8.GetString(bytes, index, chars);
+  UTFEncoding:= TEncoding.UTF8;
+  theseBytes := Copy(bytes, index, chars);
+  try
+    result :=UTFEncoding.GetString(theseBytes);
+  except
+    writeln(result)
+  end;
   {$ENDIF}
 end;
 

library/ftx/ftx_sct_services.pas

@@ -58,7 +58,7 @@
 }
 
 Uses
-  SysUtils, Classes, Generics.Collections, Character,
+  SysUtils, Classes, Generics.Collections, Character, Dialogs,
   fsl_base, fsl_utilities, fsl_collections, fsl_http, fsl_fpc, fsl_threads, fsl_lang,
   fhir_objects, fhir_common, fhir_factory, fhir_utilities, fhir_features, fhir_uris,
   fhir_cdshooks,
@@ -840,7 +840,7 @@ function TSnomedStrings.GetEntry(iIndex: Cardinal): String;
   if FIsUTF16 then
     result := memU16ToString(FMaster, iIndex+2, i)
   else
-  result := memU8ToString(FMaster, iIndex+2, i)
+    result := memU8ToString(FMaster, iIndex+2, i)
 end;
 
 procedure TSnomedStrings.Reopen;
@@ -852,15 +852,16 @@ procedure TSnomedStrings.Reopen;
 function TSnomedStrings.AddString(const s: String): Cardinal;
 var
   i : word;
-  b : TArray<Byte>;
+  b : TBytes;
 begin
   if Length(s) > 65535 Then
     raise ETerminologySetup.Create('Snomed Description too long: '+String(s));
   result := FBuilder.Length;
   if FIsUTF16 then
     b := TEncoding.BigEndianUnicode.GetBytes(s)
-  else
-    b := TEncoding.UTF8.GetBytes(s);
+    else
+    b := TEncoding.UTF8.GetBytes(s) ;
+
   i := length(b);
   FBuilder.AddWord(i);
   FBuilder.Append(b);

server/fhirconsole.lpi

@@ -143,6 +143,9 @@
               </Win32>
             </Options>
           </Linking>
+          <Other>
+            <Compiler>-O2 -Xs</Compiler>
+          </Other>
         </CompilerOptions>
       </Item4>
       <Item5 Name="osx">

server/fhirserver.lpi

@@ -168,6 +168,7 @@
               <ShowNotes Value="False"/>
               <ShowHints Value="False"/>
             </Verbosity>
+            <Compiler>-O2 -Xs</Compiler>
             <CompilerMessages>
               <IgnoredMessages idx5094="True" idx5093="True" idx5092="True" idx5091="True" idx5090="True" idx5089="True" idx5024="True"/>
             </CompilerMessages>

server/web_base.pas

@@ -432,7 +432,9 @@ function TFHIRWebServerBase.IsTerminologyServerOnly: boolean;
     result := 'video/mpeg'
   Else if AExt = '.js' Then
     result := 'text/javascript'
-  Else
+  else if AExt = '.html' then  // Add this case
+    result := 'text/html'      // Use 'text/html' for .html files
+  else
   Begin
 {$IFDEF WINDOWS}
     Try

server/web_server.pas

@@ -677,7 +677,18 @@ procedure TFhirWebServer.PlainRequest(AContext: TIdContext;
   ok : boolean;
   epn, cid, ip : String;
   tt : TTimeTracker;
+  fullPath: String;
+  DefaultFiles: array[0..2] of String;
+  DefaultFile: String;
+  i: Integer;
+
 begin
+
+  DefaultFiles[0] := 'index.html';
+  DefaultFiles[1] := 'index.htm';
+  DefaultFiles[2] := 'default.html';
+
+
   // when running with a reverse proxy, it's easier to let the reverse proxy just use non-ssl upstream, and pass through the certificate details se we know SSL is being used
   if (Common.SSLHeaderValue <> '') and (request.RawHeaders.Values['X-Client-SSL'] = Common.SSLHeaderValue) then
     SecureRequest(aContext, request, response)
@@ -742,6 +753,23 @@ procedure TFhirWebServer.PlainRequest(AContext: TIdContext;
 
           if not ok then
           begin
+            // Get full path of the requested document
+            fullPath := SourceProvider.AltFile(request.Document, '/');
+
+            // If the path corresponds to a directory, look for a default file
+            if DirectoryExists(fullPath) then
+            begin
+              for i := 0 to 2 do
+              begin
+                DefaultFile := DefaultFiles[i];
+                if FileExists(fullPath + '/' + DefaultFile) then
+                begin
+                  ReturnSpecFile(response, request.Document + '/' + DefaultFile, fullPath + '/' + DefaultFile, false);
+                  Exit;  // Exit the procedure after serving a default file
+                end;
+              end;
+            end;
+
             if request.Document = '/diagnostics' then
             begin
               epn := 'WS';

toolkit2/fhirtoolkit.lpi

@@ -118,6 +118,7 @@
             <CompilerMessages>
               <IgnoredMessages idx5024="True"/>
             </CompilerMessages>
+            <Compiler>-O2 -Xs</Compiler>
           </Other>
         </CompilerOptions>
       </Item>

utilities/codescan/codescan.lpi

@@ -53,6 +53,9 @@
             <TargetCPU Value="x86_64"/>
             <TargetOS Value="linux"/>
           </CodeGeneration>
+          <Other>
+            <Compiler>-O2 -Xs</Compiler>
+          </Other>
         </CompilerOptions>
       </Item>
       <Item Name="osx">