Date filtering repository retrieve provider

.github/workflows/cdr_cr_check/trigger_and_poll_gitlab.py

@@ -16,7 +16,7 @@
     sys.exit(1)
 
 if not project_api_read_token :
-    print("CDR-CR failed to run because READ_API_TOKEN was not set")
+    print("CDR-CR failed to run because READ_API_TOKEN (GITLAB_READ_API_TOKEN) was not set")
     sys.exit(1)
 
 # Enable logging

.github/workflows/compile_against_cdr-cr.yml

@@ -30,7 +30,7 @@ jobs:
       working-directory: ./.github/workflows/cdr_cr_check
       env:
         TRIGGER_TOKEN: ${{ secrets.GITLAB_TRIGGER_TOKEN }}
-        READ_API_TOKEN: ${{ secrets.GITLAB_READ_API_TOKEN }}
+        READ_API_TOKEN: ${{ secrets.GITLAB_READ_API_TOKEN_V2 }}
         CLINICAL_REASONING_BRANCH: ${{ github.head_ref || github.ref_name }}
         # When run via the manual run, this will be set. When run in a PR, it will be blank.
         CDR_CR_BRANCH: ${{ inputs.cdr_cr_branch }}

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/engine/retrieve/BaseRetrieveProvider.java

@@ -8,6 +8,7 @@
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
+import ca.uhn.fhir.rest.param.CompositeParam;
 import ca.uhn.fhir.rest.param.DateParam;
 import ca.uhn.fhir.rest.param.InternalCodingDt;
 import ca.uhn.fhir.rest.param.ParamPrefixEnum;
@@ -16,11 +17,11 @@
 import ca.uhn.fhir.rest.param.TokenParamModifier;
 import ca.uhn.fhir.rest.param.UriParam;
 import ca.uhn.fhir.util.ExtensionUtil;
+import com.google.common.collect.Multimap;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Date;
 import java.util.List;
-import java.util.Map;
 import java.util.Optional;
 import java.util.function.Predicate;
 import org.apache.commons.lang3.StringUtils;
@@ -52,12 +53,14 @@ public abstract class BaseRetrieveProvider implements RetrieveProvider {
     private final RetrieveSettings retrieveSettings;
     private final TerminologyProvider terminologyProvider;
     private final SearchParameterResolver resolver;
+    private final FhirContext fhirContext;
 
     protected BaseRetrieveProvider(
             final FhirContext fhirContext,
             final TerminologyProvider terminologyProvider,
             final RetrieveSettings retrieveSettings) {
         requireNonNull(fhirContext, "fhirContext can not be null.");
+        this.fhirContext = fhirContext;
         fhirVersion = fhirContext.getVersion().getVersion();
         this.retrieveSettings = requireNonNull(retrieveSettings, "retrieveSettings can not be null");
         this.terminologyProvider = requireNonNull(terminologyProvider, "terminologyProvider can not be null");
@@ -297,7 +300,7 @@ private String getValueSetFromCode(
     }
 
     public void populateTemplateSearchParams(
-            Map<String, List<IQueryParameterType>> searchParams, final String dataType, final String templateId) {
+            Multimap<String, List<IQueryParameterType>> searchParams, final String dataType, final String templateId) {
         if (getRetrieveSettings().getProfileMode() != PROFILE_MODE.OFF
                 && StringUtils.isNotBlank(templateId)
                 && !templateId.startsWith("http://hl7.org/fhir/StructureDefinition/%s".formatted(dataType))) {
@@ -309,7 +312,7 @@ public void populateTemplateSearchParams(
     }
 
     public void populateContextSearchParams(
-            Map<String, List<IQueryParameterType>> searchParams,
+            Multimap<String, List<IQueryParameterType>> searchParams,
             final String dataType,
             final String context,
             final String contextPath,
@@ -332,7 +335,7 @@ public void populateContextSearchParams(
     }
 
     public void populateTerminologySearchParams(
-            Map<String, List<IQueryParameterType>> searchParams,
+            Multimap<String, List<IQueryParameterType>> searchParams,
             final String dataType,
             final String codePath,
             final Iterable<Code> codes,
@@ -390,13 +393,13 @@ protected boolean inModifierSupported(String valueSet, String resourceName, Stri
     }
 
     public void populateDateSearchParams(
-            Map<String, List<IQueryParameterType>> searchParams,
+            Multimap<String, List<IQueryParameterType>> searchParams,
             final String dataType,
-            final String datePath,
+            final String dateParamName,
             final String dateLowPath,
             final String dateHighPath,
             final Interval dateRange) {
-        if (datePath == null && dateHighPath == null && dateRange == null) {
+        if (dateParamName == null && dateHighPath == null && dateRange == null) {
             return;
         }
 
@@ -418,14 +421,14 @@ public void populateDateSearchParams(
                             + dateRange.getStart().getClass().getSimpleName());
         }
 
-        if (StringUtils.isNotBlank(datePath)) {
-            List<IQueryParameterType> dateRangeParam = new ArrayList<>();
-            DateParam dateParam = new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, start);
-            dateRangeParam.add(dateParam);
-            dateParam = new DateParam(ParamPrefixEnum.LESSTHAN_OR_EQUALS, end);
-            dateRangeParam.add(dateParam);
-            var sp = this.resolver.getSearchParameterDefinition(dataType, datePath);
-            searchParams.put(sp.getName(), dateRangeParam);
+        if (StringUtils.isNotBlank(dateParamName)) {
+            var sp = this.resolver.getSearchParameterDefinition(dataType, dateParamName);
+
+            // a date range is a search && condition - so we'll use a composite
+            DateParam gte = new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, start);
+            DateParam lte = new DateParam(ParamPrefixEnum.LESSTHAN_OR_EQUALS, end);
+
+            searchParams.put(sp.getName(), List.of(new CompositeParam<>(gte, lte)));
         } else if (StringUtils.isNotBlank(dateLowPath)) {
             List<IQueryParameterType> dateRangeParam = new ArrayList<>();
             DateParam dateParam = new DateParam(ParamPrefixEnum.GREATERTHAN_OR_EQUALS, start);

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/engine/retrieve/FederatedDataProvider.java

@@ -17,6 +17,22 @@ public FederatedDataProvider(ModelResolver modelResolver, List<RetrieveProvider>
         this.retrieveProviders = retrieveProviders;
     }
 
+    /**
+     *
+     * @param context - resource type
+     * @param contextPath -
+     * @param contextValue - id
+     * @param dataType - resource type
+     * @param templateId
+     * @param codePath
+     * @param codes
+     * @param valueSet
+     * @param datePath - the SP name to use
+     * @param dateLowPath - high path (period.start)
+     * @param dateHighPath - low path (period.end)
+     * @param dateRange - date range to search within
+     * @return
+     */
     @Override
     public Iterable<Object> retrieve(
             String context,

cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/engine/retrieve/RepositoryRetrieveProvider.java

@@ -5,8 +5,9 @@
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.repository.IRepository;
+import com.google.common.collect.HashMultimap;
+import com.google.common.collect.Multimap;
 import java.util.Collections;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.function.Predicate;
@@ -21,6 +22,18 @@
 import org.opencds.cqf.fhir.utility.repository.ig.IgRepository;
 
 public class RepositoryRetrieveProvider extends BaseRetrieveProvider {
+
+    private class SearchConfig {
+
+        /**
+         * Each element of each list is OR'd
+         * Each
+         */
+        public Multimap<String, List<IQueryParameterType>> searchParams = HashMultimap.create();
+
+        public Predicate<IBaseResource> filter = x -> true;
+    }
+
     private final IRepository repository;
     private final FhirContext fhirContext;
 
@@ -126,20 +139,12 @@ private void configureDates(
         switch (mode) {
             case FILTER_IN_MEMORY:
             case AUTO: // TODO: offload detection based on CapabilityStatement
-                if (datePath != null) {
-                    throw new UnsupportedOperationException("in-memory dateFilters are not supported");
-                }
-                break;
             case USE_SEARCH_PARAMETERS:
                 populateDateSearchParams(config.searchParams, dataType, datePath, dateLowPath, dateHighPath, dateRange);
+                break;
         }
     }
 
-    private class SearchConfig {
-        public Map<String, List<IQueryParameterType>> searchParams = new HashMap<>();
-        public Predicate<IBaseResource> filter = x -> true;
-    }
-
     @Override
     protected boolean inModifierSupported(String valueSet, String resourceName, String searchParamName) {
         // The IN modifier is not currently supported by the ResourceMatcher used by the InMemoryRepository