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Merged
lmsurpre merged 8 commits into from
Nov 9, 2021
Merged

issues #1625 and #1596 - apply search parameter filters on init #2942

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2da196b
issues #1625 and #1596 - apply search parameter filters on init
lmsurpre Nov 5, 2021
04afd93
JDBC test cleanup
lmsurpre Nov 5, 2021
bcc1a6b
Handle missing config more gracefully
lmsurpre Nov 5, 2021
177a2af
updated documentation to reflect new behavior
lmsurpre Nov 5, 2021
146cc08
General cleanup
lmsurpre Nov 5, 2021
4b9a036
Update SearchUtil.getSearchParameters method sig
lmsurpre Nov 5, 2021
6eb594e
Update ParametersMap to store disambiguated results
lmsurpre Nov 5, 2021
53da524
minor updates per review feedback
lmsurpre Nov 5, 2021
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68 changes: 36 additions & 32 deletions ...l/src/main/java/com/ibm/fhir/cql/engine/retrieve/SearchParameterFHIRRetrieveProvider.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
import com.ibm.fhir.cql.engine.searchparam.TokenParameter;
import com.ibm.fhir.model.resource.SearchParameter;
import com.ibm.fhir.model.type.code.SearchParamType;
import com.ibm.fhir.model.util.ModelSupport;
import com.ibm.fhir.search.SearchConstants;
import com.ibm.fhir.search.SearchConstants.Prefix;

Expand Down Expand Up @@ -72,18 +73,24 @@ public int getMaxCodesPerQuery() {
return this.maxCodesPerQuery;
}

protected abstract Iterable<Object> executeQueries(String dataType, List<SearchParameterMap> queries) throws Exception;
protected abstract Iterable<Object> executeQueries(String resourceType, List<SearchParameterMap> queries) throws Exception;

@Override
public Iterable<Object> retrieve(String context, String contextPath, Object contextValue, String dataType,
String templateId, String codePath, Iterable<Code> codes, String valueSet, String datePath,
String dateLowPath, String dateHighPath, Interval dateRange) {

if (!ModelSupport.isResourceType(dataType)) {
Comment thread
prb112 marked this conversation as resolved.
throw new IllegalArgumentException("'" + dataType + "' is not a valid resource type;"
+ " SearchParameterFHIRRetrieveProvider can only retrieve FHIR resource data");
}
String resourceType = dataType;

try {
List<SearchParameterMap> queries =
this.setupQueries(context, contextPath, contextValue, dataType, templateId, codePath, codes, valueSet, datePath, dateLowPath, dateHighPath, dateRange);
this.setupQueries(context, contextPath, contextValue, resourceType, templateId, codePath, codes, valueSet, datePath, dateLowPath, dateHighPath, dateRange);

return this.executeQueries(dataType, queries);
return this.executeQueries(resourceType, queries);
} catch (RuntimeException rex) {
throw rex;
} catch (Exception ex) {
Expand All @@ -92,28 +99,27 @@ public Iterable<Object> retrieve(String context, String contextPath, Object cont
}

protected List<SearchParameterMap> setupQueries(String context, String contextPath, Object contextValue,
String dataType, String templateId, String codePath, Iterable<Code> codes, String valueSet, String datePath,
String resourceType, String templateId, String codePath, Iterable<Code> codes, String valueSet, String datePath,
String dateLowPath, String dateHighPath, Interval dateRange) throws Exception {

List<SearchParameterMap> queries = null;

Pair<String, IQueryParameter> templateParam = this.getTemplateParam(dataType, templateId);
Pair<String, IQueryParameter> contextParam = this.getContextParam(dataType, context, contextPath, contextValue);
Pair<String, DateRangeParameter> dateRangeParam = this.getDateRangeParam(dataType, datePath, dateLowPath, dateHighPath, dateRange);
Pair<String, List<IQueryParameterOr<?>>> codeParams = this.getCodeParams(dataType, codePath, codes, valueSet);
Pair<String, IQueryParameter> templateParam = this.getTemplateParam(resourceType, templateId);
Pair<String, IQueryParameter> contextParam = this.getContextParam(resourceType, context, contextPath, contextValue);
Pair<String, DateRangeParameter> dateRangeParam = this.getDateRangeParam(resourceType, datePath, dateLowPath, dateHighPath, dateRange);
Pair<String, List<IQueryParameterOr<?>>> codeParams = this.getCodeParams(resourceType, codePath, codes, valueSet);

// In the case we filtered to a valueSet without codes, there are no possible
// results.
// In the case we filtered to a valueSet without codes, there are no possible results.
if (valueSet != null && (codeParams == null || codeParams.getValue().isEmpty())) {
queries = Collections.emptyList();
} else {
queries = this.innerSetupQueries(dataType, templateParam, contextParam, dateRangeParam, codeParams);
queries = this.innerSetupQueries(resourceType, templateParam, contextParam, dateRangeParam, codeParams);
}

return queries;
}

protected List<SearchParameterMap> innerSetupQueries(String dataType, Pair<String, IQueryParameter> templateParam,
protected List<SearchParameterMap> innerSetupQueries(String resourceType, Pair<String, IQueryParameter> templateParam,
Pair<String, IQueryParameter> contextParam, Pair<String, DateRangeParameter> dateRangeParam,
Pair<String, List<IQueryParameterOr<?>>> codeParams) throws Exception {

Expand All @@ -134,30 +140,30 @@ protected List<SearchParameterMap> innerSetupQueries(String dataType, Pair<Strin
return result;
}

protected Pair<String, IQueryParameter> getTemplateParam(String dataType, String templateId) {
protected Pair<String, IQueryParameter> getTemplateParam(String resourceType, String templateId) {
// purposefully empty
return null;
}

protected Pair<String, IQueryParameter> getContextParam(String dataType, String context, String contextPath,
Object contextValue) throws Exception {
protected Pair<String, IQueryParameter> getContextParam(String resourceType, String context, String contextPath,
Object contextValue) throws Exception {
Pair<String, IQueryParameter> result = null;

if (context != null && "Patient".equals(context) && contextValue != null && contextPath != null) {
result = searchParameterResolver.createSearchParameter(context, dataType, contextPath, (String) contextValue);
result = searchParameterResolver.createSearchParameter(context, resourceType, contextPath, (String) contextValue);
if (result == null) {
throw new IllegalArgumentException(String.format("Could not resolve search parameter for dataType '%s' and contextPath '%s'", dataType, contextPath));
throw new IllegalArgumentException(String.format("Could not resolve search parameter for resourceType '%s' and contextPath '%s'", resourceType, contextPath));
}
}

return result;
}

protected Pair<String, DateRangeParameter> getDateRangeParam(String dataType, String datePath, String dateLowPath,
String dateHighPath, Interval dateRange) throws Exception {
protected Pair<String, DateRangeParameter> getDateRangeParam(String resourceType, String datePath, String dateLowPath,
String dateHighPath, Interval dateRange) throws Exception {
Pair<String, DateRangeParameter> result = null;
if (datePath != null) {
SearchParameter dateParam = this.searchParameterResolver.getSearchParameterDefinition(dataType, datePath, SearchParamType.DATE);
SearchParameter dateParam = this.searchParameterResolver.getSearchParameterDefinition(resourceType, datePath, SearchParamType.DATE);
if (dateParam != null) {
String name = dateParam.getName().getValue();

Expand All @@ -182,35 +188,33 @@ protected Pair<String, DateRangeParameter> getDateRangeParam(String dataType, St

result = Pair.of(name, rangeParam);
} else {
throw new UnsupportedOperationException(String.format("Could not resolve a search parameter with date type for %s.%s ", dataType, datePath));
throw new UnsupportedOperationException(String.format("Could not resolve a search parameter with date type for %s.%s ", resourceType, datePath));
}
}
return result;
}

protected Pair<String, List<IQueryParameterOr<?>>> getCodeParams(String dataType, String codePath, Iterable<Code> codes,
String valueSet) throws Exception {
protected Pair<String, List<IQueryParameterOr<?>>> getCodeParams(String resourceType, String codePath, Iterable<Code> codes,
String valueSet) throws Exception {

Pair<String, List<IQueryParameterOr<?>>> result = null;

if (codePath != null) {
SearchParameter searchParam = searchParameterResolver.getSearchParameterDefinition(dataType, codePath, SearchParamType.TOKEN);
SearchParameter searchParam = searchParameterResolver.getSearchParameterDefinition(resourceType, codePath, SearchParamType.TOKEN);
if (searchParam != null) {
String name = searchParam.getName().getValue();
result = Pair.of(name, getCodeParams(name, codes, valueSet));
} else {
throw new IllegalArgumentException(String.format("Could not resolve search parameter for dataType '%s' and codePath '%s'", dataType, codePath));
throw new IllegalArgumentException(String.format("Could not resolve search parameter for resourceType '%s' and codePath '%s'", resourceType, codePath));
}
}

return result;
}

// The code params will be either the literal set of codes in the event the data
// server doesn't have the referenced ValueSet
// (or doesn't support pulling and caching a ValueSet).
// If the target server DOES support that then it's "dataType.codePath in
// ValueSet"
// server doesn't have the referenced ValueSet (or doesn't support pulling and caching a ValueSet).
// If the target server DOES support that then it's "resourceType.codePath in ValueSet"
protected List<IQueryParameterOr<?>> getCodeParams(String name, Iterable<Code> codes, String valueSet) {
List<IQueryParameterOr<?>> params = null;

Expand Down Expand Up @@ -260,7 +264,7 @@ protected List<IQueryParameterOr<?>> getCodeParams(String name, Iterable<Code> c
}

protected SearchParameterMap getBaseMap(Pair<String, IQueryParameter> templateParam,
Pair<String, IQueryParameter> contextParam, Pair<String, DateRangeParameter> dateRangeParam) throws Exception {
Pair<String, IQueryParameter> contextParam, Pair<String, DateRangeParameter> dateRangeParam) throws Exception {

SearchParameterMap searchParameters = new SearchParameterMap();
// baseMap.setLastUpdated(new DateRangeParam());
Expand All @@ -283,11 +287,11 @@ protected SearchParameterMap getBaseMap(Pair<String, IQueryParameter> templatePa

return searchParameters;
}

/**
* Given a query parameter name and contents, transmute the name
* into something that includes all the appropriate modifiers.
*
*
* @param name query parameter name
* @param param query parameter contents
* @return query parameter name with appropriate modifiers appended
Expand Down
32 changes: 17 additions & 15 deletions cql/fhir-cql/src/main/java/com/ibm/fhir/cql/engine/searchparam/SearchParameterResolver.java
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;

import org.apache.commons.lang3.tuple.Pair;
Expand All @@ -20,13 +21,13 @@

public class SearchParameterResolver {

public SearchParameter getSearchParameterDefinition(String dataType, String path) throws Exception {
return getSearchParameterDefinition(dataType, path, null);
public SearchParameter getSearchParameterDefinition(String resourceType, String path) throws Exception {
return getSearchParameterDefinition(resourceType, path, null);
}

public SearchParameter getSearchParameterDefinition(String dataType, String path, SearchParamType paramType)
throws Exception {
if (dataType == null || path == null) {
public SearchParameter getSearchParameterDefinition(String resourceType, String path, SearchParamType paramType)
throws Exception {
if (resourceType == null || path == null) {
return null;
}

Expand All @@ -36,15 +37,16 @@ public SearchParameter getSearchParameterDefinition(String dataType, String path
path = "";
}

List<SearchParameter> params = SearchUtil.getApplicableSearchParameters(dataType);
// XXX should this use the registry (all parameters) or the filtered set of search parameters for a given tenant?
Map<String, SearchParameter> params = SearchUtil.getSearchParameters(resourceType);

for (SearchParameter param : params) {
for (SearchParameter param : params.values()) {
if (name != null && param.getName().getValue().equals(name)) {
return param;
}

if (paramType == null || param.getType().equals(paramType)) {
Set<String> normalizedPath = normalizePath(dataType, param.getExpression().getValue());
Set<String> normalizedPath = normalizePath(resourceType, param.getExpression().getValue());
Comment thread
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if (normalizedPath.contains(path)) {
return param;
}
Expand All @@ -54,12 +56,12 @@ public SearchParameter getSearchParameterDefinition(String dataType, String path
return null;
}

public Pair<String, IQueryParameter> createSearchParameter(String context, String dataType, String path, String value)
throws Exception {
public Pair<String, IQueryParameter> createSearchParameter(String context, String resourceType, String path, String value)
throws Exception {

Pair<String, IQueryParameter> result = null;

SearchParameter searchParam = this.getSearchParameterDefinition(dataType, path);
SearchParameter searchParam = this.getSearchParameterDefinition(resourceType, path);
if (searchParam != null) {

String name = searchParam.getName().getValue();
Expand All @@ -86,7 +88,7 @@ public Pair<String, IQueryParameter> createSearchParameter(String context, Strin

// This is actually a lot of processing. We should cache search parameter
// resolutions.
private Set<String> normalizePath(String dataType, String path) {
private Set<String> normalizePath(String resourceType, String path) {
// TODO: What we really need is FhirPath parsing to just get the path
// MedicationAdministration.medication.as(CodeableConcept)
// MedicationAdministration.medication.as(Reference)
Expand All @@ -105,7 +107,7 @@ private Set<String> normalizePath(String dataType, String path) {
part = removeParens(part);

// Trim off DataType
if (part.startsWith(dataType)) {
if (part.startsWith(resourceType)) {
part = part.substring(part.indexOf(".") + 1, part.length());

// Split into components
Expand Down Expand Up @@ -148,8 +150,8 @@ private Set<String> normalizePath(String dataType, String path) {
// }
return normalizedParts;
}
private String removeParens(String path) {

private String removeParens(String path) {
if (path.startsWith("(")) {
path = path.substring(1, path.length() - 1);
}
Expand Down
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