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Merge remote-tracking branch
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'origin/issue/175_Template_Engine_for_HTML_UIs' into develop
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hhund committed Feb 21, 2024
2 parents 7311625 + 50031a2 commit cb3d00f
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Showing 37 changed files with 748 additions and 247 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -312,8 +312,7 @@ private ProcessDefinition getProcessDefinition(String processDomain, String proc
if (processVersion != null && !processVersion.isBlank())
return repositoryService.createProcessDefinitionQuery().active()
.processDefinitionKey(processDomain + "_" + processDefinitionKey).versionTag(processVersion).list()
.stream().sorted(Comparator.comparing(ProcessDefinition::getVersion).reversed()).findFirst()
.orElse(null);
.stream().max(Comparator.comparing(ProcessDefinition::getVersion)).orElse(null);
else
return repositoryService.createProcessDefinitionQuery().active()
.processDefinitionKey(processDomain + "_" + processDefinitionKey).latestVersion().singleResult();
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Expand Up @@ -4,6 +4,7 @@
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.Base64;
import java.util.Comparator;
import java.util.Objects;
import java.util.function.Consumer;

Expand Down Expand Up @@ -101,7 +102,8 @@ private ProcessDefinition getProcessDefinition(String processDefinitionKey, Stri
{
if (versionTag != null && !versionTag.isBlank())
return repositoryService.createProcessDefinitionQuery().processDefinitionKey(processDefinitionKey)
.versionTag(versionTag).singleResult();
.versionTag(versionTag).list().stream().max(Comparator.comparing(ProcessDefinition::getVersion))
.orElse(null);
else
return repositoryService.createProcessDefinitionQuery().processDefinitionKey(processDefinitionKey)
.latestVersion().singleResult();
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Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,7 @@ private List<ProcessEntry> processes()
return repositoryService.createProcessDefinitionQuery().active().unlimitedList().stream()
.map(def -> new ProcessEntry("Process/" + def.getKey() + "/" + def.getVersionTag(),
def.getKey() + " | " + def.getVersionTag()))
.sorted(Comparator.comparing(ProcessEntry::value)).toList();
.sorted(Comparator.comparing(ProcessEntry::value)).distinct().toList();
}

private List<String> processInstances()
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Expand Up @@ -96,9 +96,9 @@ protected void doSetVariables(BiConsumer<String, Object> variables, Bundle resou

int currentPage = getPage(params);
int count = getCount(params, defaultPageCount);
int maxPages = (int) Math.ceil((double) resource.getTotal() / count);
int maxPages = count <= 0 ? 0 : (int) Math.ceil((double) resource.getTotal() / count);
int offset = Math.multiplyExact(currentPage - 1, count);
int firstResource = Integer.MAX_VALUE - 1 < offset ? 0 : offset + 1;
int firstResource = count == 0 ? 0 : Integer.MAX_VALUE - 1 < offset ? 0 : offset + 1;
int lastResource = Integer.MAX_VALUE - matchResources.size() < offset ? 0 : offset + matchResources.size();

long includeResources = resource.getEntry().stream().filter(
Expand Down Expand Up @@ -142,11 +142,11 @@ private int getPage(MultivaluedMap<String, String> params)
}
catch (NumberFormatException e)
{
return 1;
return 0;
}
}
else
return 1;
return 0;
}

private int getCount(MultivaluedMap<String, String> params, int defaultPageCount)
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@
import dev.dsf.fhir.dao.ResourceDao;
import dev.dsf.fhir.dao.provider.DaoProvider;
import dev.dsf.fhir.help.ParameterConverter;
import dev.dsf.fhir.search.PageAndCount;
import dev.dsf.fhir.search.PartialResult;
import dev.dsf.fhir.search.SearchQuery;
import dev.dsf.fhir.search.SearchQueryParameterError;
Expand Down Expand Up @@ -189,7 +190,7 @@ protected final boolean organizationWithIdentifierExists(Connection connection,
Map<String, List<String>> queryParameters = Map.of("identifier",
Collections.singletonList(iSystem + "|" + iValue));
OrganizationDao dao = daoProvider.getOrganizationDao();
SearchQuery<Organization> query = dao.createSearchQueryWithoutUserFilter(0, 0)
SearchQuery<Organization> query = dao.createSearchQueryWithoutUserFilter(PageAndCount.exists())
.configureParameters(queryParameters);

List<SearchQueryParameterError> uQp = query.getUnsupportedQueryParameters();
Expand Down Expand Up @@ -223,7 +224,7 @@ protected final boolean roleExists(Connection connection, Coding coding)
Map<String, List<String>> queryParameters = Map.of("url",
Collections.singletonList(cSystem + (coding.hasVersion() ? "|" + cVersion : "")));
CodeSystemDao dao = daoProvider.getCodeSystemDao();
SearchQuery<CodeSystem> query = dao.createSearchQueryWithoutUserFilter(1, 1)
SearchQuery<CodeSystem> query = dao.createSearchQueryWithoutUserFilter(PageAndCount.single())
.configureParameters(queryParameters);

List<SearchQueryParameterError> uQp = query.getUnsupportedQueryParameters();
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Expand Up @@ -21,6 +21,7 @@
import dev.dsf.fhir.dao.EndpointDao;
import dev.dsf.fhir.dao.provider.DaoProvider;
import dev.dsf.fhir.help.ParameterConverter;
import dev.dsf.fhir.search.PageAndCount;
import dev.dsf.fhir.search.PartialResult;
import dev.dsf.fhir.search.SearchQuery;
import dev.dsf.fhir.search.SearchQueryParameterError;
Expand All @@ -31,7 +32,7 @@ public class EndpointAuthorizationRule extends AbstractMetaTagAuthorizationRule<
private static final Logger logger = LoggerFactory.getLogger(EndpointAuthorizationRule.class);

private static final String ENDPOINT_IDENTIFIER_SYSTEM = "http://dsf.dev/sid/endpoint-identifier";
private static final String ENDPOINT_ADDRESS_PATTERN_STRING = "https://([0-9a-zA-Z\\.-]+)+(:\\d{1,4})?([-\\w/]*)";
private static final String ENDPOINT_ADDRESS_PATTERN_STRING = "https://[0-9a-zA-Z.-]+(?::\\d{1,4})?[-\\w/]*";
private static final Pattern ENDPOINT_ADDRESS_PATTERN = Pattern.compile(ENDPOINT_ADDRESS_PATTERN_STRING);

public EndpointAuthorizationRule(DaoProvider daoProvider, String serverBase, ReferenceResolver referenceResolver,
Expand Down Expand Up @@ -111,7 +112,8 @@ private boolean endpointWithAddressExists(Connection connection, String address)
{
Map<String, List<String>> queryParameters = Map.of("address", Collections.singletonList(address));
EndpointDao dao = getDao();
SearchQuery<Endpoint> query = dao.createSearchQueryWithoutUserFilter(0, 0).configureParameters(queryParameters);
SearchQuery<Endpoint> query = dao.createSearchQueryWithoutUserFilter(PageAndCount.exists())
.configureParameters(queryParameters);

List<SearchQueryParameterError> uQp = query.getUnsupportedQueryParameters();
if (!uQp.isEmpty())
Expand Down Expand Up @@ -140,7 +142,8 @@ private boolean endpointWithIdentifierExists(Connection connection, String ident
Map<String, List<String>> queryParameters = Map.of("identifier",
Collections.singletonList(ENDPOINT_IDENTIFIER_SYSTEM + "|" + identifierValue));
EndpointDao dao = getDao();
SearchQuery<Endpoint> query = dao.createSearchQueryWithoutUserFilter(0, 0).configureParameters(queryParameters);
SearchQuery<Endpoint> query = dao.createSearchQueryWithoutUserFilter(PageAndCount.exists())
.configureParameters(queryParameters);

List<SearchQueryParameterError> uQp = query.getUnsupportedQueryParameters();
if (!uQp.isEmpty())
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@
import dev.dsf.fhir.dao.OrganizationAffiliationDao;
import dev.dsf.fhir.dao.provider.DaoProvider;
import dev.dsf.fhir.help.ParameterConverter;
import dev.dsf.fhir.search.PageAndCount;
import dev.dsf.fhir.search.PartialResult;
import dev.dsf.fhir.search.SearchQuery;
import dev.dsf.fhir.search.SearchQueryParameterError;
Expand Down Expand Up @@ -154,7 +155,7 @@ private Map<String, List<String>> queryParameters(OrganizationAffiliation newRes
private boolean organizationAffiliationExists(Connection connection, Map<String, List<String>> queryParameters)
{
OrganizationAffiliationDao dao = getDao();
SearchQuery<OrganizationAffiliation> query = dao.createSearchQueryWithoutUserFilter(0, 0)
SearchQuery<OrganizationAffiliation> query = dao.createSearchQueryWithoutUserFilter(PageAndCount.exists())
.configureParameters(queryParameters);

List<SearchQueryParameterError> uQp = query.getUnsupportedQueryParameters();
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
import dev.dsf.fhir.dao.SubscriptionDao;
import dev.dsf.fhir.dao.provider.DaoProvider;
import dev.dsf.fhir.help.ParameterConverter;
import dev.dsf.fhir.search.PageAndCount;
import dev.dsf.fhir.search.PartialResult;
import dev.dsf.fhir.search.SearchQuery;
import dev.dsf.fhir.search.SearchQueryParameterError;
Expand Down Expand Up @@ -87,7 +88,8 @@ private Optional<String> newResourceOk(Connection connection, Subscription newRe
Optional<ResourceDao<?>> optDao = daoProvider.getDao(cComponentes.getPathSegments().get(0));
if (optDao.isPresent())
{
SearchQuery<?> searchQuery = optDao.get().createSearchQueryWithoutUserFilter(1, 1);
SearchQuery<?> searchQuery = optDao.get().createSearchQueryWithoutUserFilter(PageAndCount.exists())
.configureParameters(cComponentes.getQueryParams());
List<SearchQueryParameterError> uQp = searchQuery.getUnsupportedQueryParameters();
if (!uQp.isEmpty())
{
Expand Down Expand Up @@ -131,7 +133,7 @@ protected boolean resourceExists(Connection connection, Subscription newResource
Collections.singletonList(newResource.getChannel().getType().toCode()), "payload",
Collections.singletonList(newResource.getChannel().getPayload()));
SubscriptionDao dao = getDao();
SearchQuery<Subscription> query = dao.createSearchQueryWithoutUserFilter(1, 1)
SearchQuery<Subscription> query = dao.createSearchQueryWithoutUserFilter(PageAndCount.exists())
.configureParameters(queryParameters);

List<SearchQueryParameterError> uQp = query.getUnsupportedQueryParameters();
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
import dev.dsf.fhir.dao.exception.ResourceNotMarkedDeletedException;
import dev.dsf.fhir.dao.exception.ResourceVersionNoMatchException;
import dev.dsf.fhir.search.DbSearchQuery;
import dev.dsf.fhir.search.PageAndCount;
import dev.dsf.fhir.search.PartialResult;
import dev.dsf.fhir.search.SearchQuery;

Expand Down Expand Up @@ -355,9 +356,21 @@ R updateWithTransaction(Connection connection, R resource, Long expectedVersion)
*/
PartialResult<R> searchWithTransaction(Connection connection, DbSearchQuery query) throws SQLException;

SearchQuery<R> createSearchQuery(Identity identity, int page, int count);
/**
* @param identity
* not <code>null</code>
* @param pageAndCount
* not <code>null</code>
* @return query
*/
SearchQuery<R> createSearchQuery(Identity identity, PageAndCount pageAndCount);

SearchQuery<R> createSearchQueryWithoutUserFilter(int page, int count);
/**
* @param pageAndCount
* not <code>null</code>
* @return query
*/
SearchQuery<R> createSearchQueryWithoutUserFilter(PageAndCount pageAndCount);

/**
* Permanently delete a resource that was previously marked as deleted.
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@
import dev.dsf.fhir.help.ParameterConverter;
import dev.dsf.fhir.help.ResponseGenerator;
import dev.dsf.fhir.prefer.PreferReturnType;
import dev.dsf.fhir.search.PageAndCount;
import dev.dsf.fhir.search.PartialResult;
import dev.dsf.fhir.search.SearchQuery;
import dev.dsf.fhir.search.SearchQueryParameterError;
Expand Down Expand Up @@ -199,7 +200,7 @@ private Optional<Resource> checkAlreadyExists(Connection connection, String ifNo
.collect(Collectors.toMap(Entry::getKey, Entry::getValue));
}

SearchQuery<R> query = dao.createSearchQueryWithoutUserFilter(1, 1);
SearchQuery<R> query = dao.createSearchQueryWithoutUserFilter(PageAndCount.single());
query.configureParameters(queryParameters);

List<SearchQueryParameterError> unsupportedQueryParameters = query.getUnsupportedQueryParameters();
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@
import dev.dsf.fhir.help.ParameterConverter;
import dev.dsf.fhir.help.ResponseGenerator;
import dev.dsf.fhir.prefer.PreferReturnType;
import dev.dsf.fhir.search.PageAndCount;
import dev.dsf.fhir.search.PartialResult;
import dev.dsf.fhir.search.SearchQuery;
import dev.dsf.fhir.search.SearchQueryParameterError;
Expand Down Expand Up @@ -172,7 +173,7 @@ private Optional<Resource> search(Connection connection, ResourceDao<?> dao,
.collect(Collectors.toMap(Entry::getKey, Entry::getValue));
}

SearchQuery<?> query = dao.createSearchQueryWithoutUserFilter(1, 1);
SearchQuery<?> query = dao.createSearchQueryWithoutUserFilter(PageAndCount.single());
query.configureParameters(queryParameters);

List<SearchQueryParameterError> unsupportedQueryParameters = query.getUnsupportedQueryParameters();
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@
import dev.dsf.fhir.help.ResponseGenerator;
import dev.dsf.fhir.prefer.PreferHandlingType;
import dev.dsf.fhir.prefer.PreferReturnType;
import dev.dsf.fhir.search.PageAndCount;
import dev.dsf.fhir.search.PartialResult;
import dev.dsf.fhir.search.SearchQuery;
import dev.dsf.fhir.search.SearchQueryParameterError;
Expand Down Expand Up @@ -193,14 +194,8 @@ private void readByCondition(Connection connection, String resourceTypeName,
responseResult = Response.status(Status.NOT_FOUND).build();
else
{
Integer page = parameterConverter.getFirstInt(cleanQueryParameters, SearchQuery.PARAMETER_PAGE);
int effectivePage = page == null ? 1 : page;

Integer count = parameterConverter.getFirstInt(cleanQueryParameters, SearchQuery.PARAMETER_COUNT);
int effectiveCount = (count == null || count < 0) ? defaultPageCount : count;

SearchQuery<? extends Resource> query = optDao.get().createSearchQuery(identity, effectivePage,
effectiveCount);
SearchQuery<? extends Resource> query = optDao.get().createSearchQuery(identity,
PageAndCount.from(cleanQueryParameters, defaultPageCount));
query.configureParameters(cleanQueryParameters);
List<SearchQueryParameterError> errors = query.getUnsupportedQueryParameters();

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@
import dev.dsf.fhir.help.ParameterConverter;
import dev.dsf.fhir.help.ResponseGenerator;
import dev.dsf.fhir.prefer.PreferReturnType;
import dev.dsf.fhir.search.PageAndCount;
import dev.dsf.fhir.search.PartialResult;
import dev.dsf.fhir.search.SearchQuery;
import dev.dsf.fhir.search.SearchQueryParameterError;
Expand Down Expand Up @@ -151,7 +152,7 @@ private boolean addMissingIdToTranslationTableAndCheckConditionFindsResource(Map
.collect(Collectors.toMap(Entry::getKey, Entry::getValue));
}

SearchQuery<R> query = dao.createSearchQueryWithoutUserFilter(1, 1);
SearchQuery<R> query = dao.createSearchQueryWithoutUserFilter(PageAndCount.single());
query.configureParameters(queryParameters);

List<SearchQueryParameterError> unsupportedParams = query.getUnsupportedQueryParameters();
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@
import dev.dsf.fhir.dao.exception.ResourceNotMarkedDeletedException;
import dev.dsf.fhir.dao.exception.ResourceVersionNoMatchException;
import dev.dsf.fhir.search.DbSearchQuery;
import dev.dsf.fhir.search.PageAndCount;
import dev.dsf.fhir.search.PartialResult;
import dev.dsf.fhir.search.SearchQuery;
import dev.dsf.fhir.search.SearchQuery.SearchQueryBuilder;
Expand Down Expand Up @@ -898,20 +899,24 @@ private void getResources(ResultSet result, int columnIndex, List<? super Resour
}

@Override
public final SearchQuery<R> createSearchQuery(Identity identity, int page, int count)
public final SearchQuery<R> createSearchQuery(Identity identity, PageAndCount pageAndCount)
{
return doCreateSearchQuery(identity, page, count);
Objects.requireNonNull(identity, "identity");

return doCreateSearchQuery(identity, pageAndCount);
}

@Override
public SearchQuery<R> createSearchQueryWithoutUserFilter(int page, int count)
public SearchQuery<R> createSearchQueryWithoutUserFilter(PageAndCount pageAndCount)
{
return doCreateSearchQuery(null, page, count);
return doCreateSearchQuery(null, pageAndCount);
}

private SearchQuery<R> doCreateSearchQuery(Identity identity, int page, int count)
private SearchQuery<R> doCreateSearchQuery(Identity identity, PageAndCount pageAndCount)
{
var builder = SearchQueryBuilder.create(resourceType, getResourceTable(), getResourceColumn(), page, count);
Objects.requireNonNull(pageAndCount, "pageAndCount");

var builder = SearchQueryBuilder.create(resourceType, getResourceTable(), getResourceColumn(), pageAndCount);

if (identity != null)
builder = builder.with(identityFilter.apply(identity));
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -186,8 +186,7 @@ public Bundle createSearchSet(PartialResult<? extends Resource> result, List<Sea

bundle.setTotal(result.getTotal());

setLinks(result.getPageAndCount(), bundleUri, format, pretty, summaryMode, bundle,
result.getPartialResult().isEmpty(), result.getTotal());
setLinks(result.getPageAndCount(), bundleUri, format, pretty, summaryMode, bundle, result.getTotal());

return bundle;
}
Expand Down Expand Up @@ -217,8 +216,7 @@ public Bundle createHistoryBundle(History history, List<SearchQueryParameterErro

bundle.setTotal(history.getTotal());

setLinks(history.getPageAndCount(), bundleUri, format, pretty, summaryMode, bundle,
history.getEntries().isEmpty(), history.getTotal());
setLinks(history.getPageAndCount(), bundleUri, format, pretty, summaryMode, bundle, history.getTotal());

return bundle;
}
Expand Down Expand Up @@ -262,7 +260,7 @@ private String toLocation(String resourceType, String id, String version)
}

private void setLinks(PageAndCount pageAndCount, UriBuilder bundleUri, String format, String pretty,
SummaryMode summaryMode, Bundle bundle, boolean isEmpty, int total)
SummaryMode summaryMode, Bundle bundle, int total)
{
if (format != null)
bundleUri = bundleUri.replaceQueryParam("_format", format);
Expand All @@ -271,17 +269,18 @@ private void setLinks(PageAndCount pageAndCount, UriBuilder bundleUri, String fo
if (summaryMode != null)
bundleUri = bundleUri.replaceQueryParam("_summary", summaryMode.toString());

if (pageAndCount.getCount() > 0)
boolean countOnly = pageAndCount.isCountOnly(total);
if (!countOnly)
{
bundleUri = bundleUri.replaceQueryParam("_count", pageAndCount.getCount());
bundleUri = bundleUri.replaceQueryParam("_page", isEmpty ? 1 : pageAndCount.getPage());
bundleUri = bundleUri.replaceQueryParam("_page", pageAndCount.getPage());
}
else
bundleUri = bundleUri.replaceQueryParam("_count", "0");

bundle.addLink().setRelation("self").setUrlElement(new UriType(bundleUri.build()));

if (pageAndCount.getCount() > 0 && !isEmpty)
if (!countOnly && pageAndCount.getCount() > 0)
{
bundleUri = bundleUri.replaceQueryParam("_page", 1);
bundleUri = bundleUri.replaceQueryParam("_count", pageAndCount.getCount());
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -87,13 +87,7 @@ public Bundle getHistory(Identity identity, UriInfo uri, HttpHeaders headers,
{
MultivaluedMap<String, String> queryParameters = uri.getQueryParameters();

Integer page = parameterConverter.getFirstInt(queryParameters, SearchQuery.PARAMETER_PAGE);
int effectivePage = page == null ? 1 : page;

Integer count = parameterConverter.getFirstInt(queryParameters, SearchQuery.PARAMETER_COUNT);
int effectiveCount = count == null || count < 0 ? defaultPageCount : count;

PageAndCount pageAndCount = new PageAndCount(effectivePage, effectiveCount);
PageAndCount pageAndCount = PageAndCount.from(uri.getQueryParameters(), defaultPageCount);

List<AtParameter> atParameters = new ArrayList<>();
SinceParameter sinceParameter = new SinceParameter();
Expand Down
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