Merge pull request #21 from HealthIntersections/master

catch up
costateixeira · Oct 21, 2024 · 45a1ff7 · 45a1ff7
2 parents 74d60f3 + 8a3c5d8
commit 45a1ff7
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Showing 4 changed files with 29 additions and 10 deletions.
diff --git a/.github/workflows/linux-docker-build.yml b/.github/workflows/linux-docker-build.yml
@@ -43,12 +43,19 @@ jobs:
           -e MYSQL_DATABASE=test \
           -d mysql:8
 
-    # Step 5: Build the Docker image and tag it for GitHub Container Registry (GHCR)
+    # Step 5: Convert repository owner and name to lowercase
+    - name: Convert repository owner and name to lowercase
+      id: vars
+      run: |
+        echo "org_name=$(echo ${{ github.repository_owner }} | tr '[:upper:]' '[:lower:]')" >> $GITHUB_ENV
+        echo "repo_name=$(basename ${{ github.repository }} | tr '[:upper:]' '[:lower:]')" >> $GITHUB_ENV
+
+    # Step 6: Build the Docker image and tag it for GitHub Container Registry (GHCR)
     - name: Docker Build
       run: |
-        docker build --tag ghcr.io/${{ github.repository_owner }}/fhirserver:nightly .
+        docker build --tag ghcr.io/${{ env.org_name }}/fhirserver:nightly .
 
-    # Step 6: Prepare ini file for your FHIR Server with environment variables
+    # Step 7: Prepare ini file for your FHIR Server with environment variables
     - name: Prepare ini file
       env:
         FHIRSERVER_LOCATIONS_CLONE_PATH: /work/fhirserver
@@ -66,14 +73,14 @@ jobs:
       run: |
         cat fixtures/test-settings.ini.template | envsubst > ~/test-settings.ini
 
-    # Step 7: Ensure SNOMED cache is present
+    # Step 8: Ensure SNOMED cache is present
     - name: Ensure SNOMED cache is present
       run: |
         mkdir -p ~/terminology/fhir-server
         wget -q --no-clobber https://storage.googleapis.com/ig-build/snomed.test.cache -O ~/terminology/fhir-server/snomed.test.cache || true
         ls ~/terminology/fhir-server/snomed.test.cache
 
-    # Step 8: Push the Docker image to GitHub Container Registry (GHCR)
+    # Step 9: Push the Docker image to GitHub Container Registry (GHCR)
     - name: Push Docker image to GHCR
       run: |
-        docker push ghcr.io/${{ github.repository_owner }}/fhirserver:nightly
+        docker push ghcr.io/${{ env.org_name }}/fhirserver:nightly
diff --git a/library/fhir/fhir_tx.pas b/library/fhir/fhir_tx.pas
@@ -335,7 +335,7 @@ procedure TTerminologyOperationContext.log(note: String);
 var
   s : string;
 begin
-  s := DescribePeriodMS(GetTickCount64 - FStartTime)+' '+note;
+  s := inttostr(GetTickCount64 - FStartTime)+'ms '+note;
   if UnderDebugger then
     Logging.log(s);
   FTimeTracker.step(s);
@@ -345,7 +345,7 @@ procedure TTerminologyOperationContext.addNote(vs : TFHIRValueSetW; note : Strin
 var
   s : string;
 begin
-  s := DescribePeriodMS(GetTickCount64 - FStartTime)+' '+vs.vurl+': '+note;
+  s := inttostr(GetTickCount64 - FStartTime)+'ms '+vs.vurl+': '+note;
   if UnderDebugger then
     Logging.log(s);
   FTimeTracker.step(s);

diff --git a/library/ftx/fhir_valuesets.pas b/library/ftx/fhir_valuesets.pas
@@ -3503,6 +3503,7 @@ procedure TFHIRValueSetExpander.includeCodes(cset: TFhirValueSetComposeIncludeW;
       begin
         //Logging.log('Processing '+vsId+', import value set '+s);
         deadCheck('processCodes#2');
+        FOpContext.log('import value set '+s);
         ivs := TFHIRImportedValueSet.create(expandValueset(s, '', filter.filter, dependencies, notClosed));
         try
           checkCanonicalStatus(expansion, ivs.FValueSet, FValueSet);
@@ -3535,6 +3536,7 @@ procedure TFHIRValueSetExpander.includeCodes(cset: TFhirValueSetComposeIncludeW;
             //Logging.log(' ...import value set '+s);
             deadCheck('processCodes#3');
             f := nil;
+            FOpContext.log('import2 value set '+s);
             // if we can, we can do a short cut evaluation that means we don't have to do a full expansion of the source value set.
             // this saves lots of overhead we don't need. But it does require simple cases (though they are common). So we have a look
             // at the value set, and see whether we can short cut it. If we can, it's just another filter (though we can't iterate on it)
@@ -3555,6 +3557,7 @@ procedure TFHIRValueSetExpander.includeCodes(cset: TFhirValueSetComposeIncludeW;
           begin
             if (cs.SpecialEnumeration <> '') and FParams.limitedExpansion and filters.Empty then
             begin
+              FOpContext.log('import special value set '+s);
               base := expandValueSet(cs.SpecialEnumeration, '', filter.filter, dependencies, notClosed);
               try
                 expansion.addExtensionV('http://hl7.org/fhir/StructureDefinition/valueset-toocostly', FFactory.makeBoolean(true));
@@ -3566,6 +3569,7 @@ procedure TFHIRValueSetExpander.includeCodes(cset: TFhirValueSetComposeIncludeW;
             end
             else if filter.Null then // special case - add all the code system
             begin
+              FOpContext.log('add whole code system');
               if cs.isNotClosed(FOpContext, filter) then
                 if cs.SpecialEnumeration <> '' then
                   raise costDiags(ETooCostly.create('The code System "'+cs.systemUri+'" has a grammar, and cannot be enumerated directly. If an incomplete expansion is requested, a limited enumeration will be returned'))
@@ -3595,6 +3599,7 @@ procedure TFHIRValueSetExpander.includeCodes(cset: TFhirValueSetComposeIncludeW;
             end
             else
             begin
+              FOpContext.log('prepare filters');
               NoTotal;
               if cs.isNotClosed(FOpContext, filter) then
                 notClosed := true;
@@ -3603,6 +3608,7 @@ procedure TFHIRValueSetExpander.includeCodes(cset: TFhirValueSetComposeIncludeW;
                 ctxt := cs.searchFilter(FOpContext, filter, prep, false);
                 try
                   cs.prepare(FOpContext, prep);
+                  FOpContext.log('iterate filters');
                   while cs.FilterMore(FOpContext, ctxt) do
                   begin
                     deadCheck('processCodes#4');
@@ -3623,6 +3629,7 @@ procedure TFHIRValueSetExpander.includeCodes(cset: TFhirValueSetComposeIncludeW;
                       c.free;
                     end;
                   end;
+                  FOpContext.log('iterate filters done');
                 finally
                   ctxt.free;
                 end;
@@ -3634,6 +3641,7 @@ procedure TFHIRValueSetExpander.includeCodes(cset: TFhirValueSetComposeIncludeW;
 
           if (cset.hasConcepts) then
           begin
+            FOpContext.log('iterate concepts');
             cds := TConceptDesignations.Create(FFactory.link, FLanguages.link);
             try
               tcount := 0;
@@ -3666,10 +3674,12 @@ procedure TFHIRValueSetExpander.includeCodes(cset: TFhirValueSetComposeIncludeW;
             finally
               cds.free;
             end;
+            FOpContext.log('iterate concepts done');
           end;
 
           if cset.hasFilters then
           begin
+            FOpContext.log('prepare filters');
             fcl := cset.filters;
             try
               prep := cs.getPrepContext(FOpContext);
@@ -3706,6 +3716,7 @@ procedure TFHIRValueSetExpander.includeCodes(cset: TFhirValueSetComposeIncludeW;
 
                 inner := cs.prepare(FOpContext, prep);
                 count := 0;
+                FOpContext.log('iterate filters');
                 While cs.FilterMore(FOpContext, filters[0]) do
                 begin
                   deadCheck('processCodes#5');
@@ -3742,6 +3753,7 @@ procedure TFHIRValueSetExpander.includeCodes(cset: TFhirValueSetComposeIncludeW;
               finally
                 prep.free;
               end;
+              FOpContext.log('iterate filters done');
             finally
               fcl.free;
             end;

diff --git a/library/ftx/ftx_loinc_services.pas b/library/ftx/ftx_loinc_services.pas
@@ -1042,9 +1042,9 @@ function TLOINCServices.filterBySQL(opContext : TTxOperationContext; c : TFDBCon
     end;
     c.terminate;
     t := GetTickCount64-t;
-    opContext.log('LOINC filter: '+inttostr(l)+' rows for '+d+' ('+DescribePeriodMS(t)+', sql = '+sql+')');
+    opContext.log('LOINC filter: '+inttostr(l)+' rows for '+d+' ('+inttostr(t)+'ms)');
     if (UnderDebugger) or (t > 1000) then
-      Logging.log('LOINC filter: '+inttostr(l)+' rows for '+d+' ('+DescribePeriodMS(t)+', sql = '+sql+')');
+      Logging.log('LOINC filter: '+inttostr(l)+' rows for '+d+' ('+inttostr(t)+'ms, sql = '+sql+')');
   end;
   SetLength(keys, l);
   result := TLoincFilterHolder.create;