diff --git a/src/server/API/API.csproj b/src/server/API/API.csproj
index aa0111a2b..b68460d17 100644
--- a/src/server/API/API.csproj
+++ b/src/server/API/API.csproj
@@ -25,6 +25,12 @@
+
+
+
+
+
+
@@ -55,5 +61,11 @@
+
+
+
+
+
+
diff --git a/src/server/API/Authorization/ShrineUserContext.cs b/src/server/API/Authorization/ShrineUserContext.cs
new file mode 100644
index 000000000..5aba9c486
--- /dev/null
+++ b/src/server/API/Authorization/ShrineUserContext.cs
@@ -0,0 +1,80 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using Model.Authorization;
+using Model.Options;
+using Model.Integration.Shrine;
+
+namespace API.Authorization
+{
+ public class ShrineUserContext : IUserContext
+ {
+ readonly ShrineResearcher researcher;
+
+ public ShrineUserContext(ShrineResearcher researcher)
+ {
+ this.researcher = researcher;
+ }
+
+ public string[] Groups { get; } = Array.Empty();
+
+ public string[] Roles { get; } = new string[] { Role.Fed };
+
+ public bool IsInRole(string role) => role == Role.Fed;
+
+ public bool IsAdmin => false;
+
+ public bool IsQuarantined => false;
+
+ public string Identity => researcher.UserName;
+
+
+ string iss;
+ public string Issuer
+ {
+ get
+ {
+ iss ??= researcher.UserDomainName;
+ return iss;
+ }
+ }
+
+ string uuid;
+ public string UUID
+ {
+ get
+ {
+ if (uuid == null)
+ {
+ var issu = Issuer;
+ var id = Identity;
+ if (id != null && issu != null)
+ {
+ uuid = $"{id}@{issu}";
+ }
+ }
+ return uuid;
+ }
+ }
+
+ public bool IsInstitutional => false;
+
+ readonly Guid idNonce = Guid.NewGuid();
+ public Guid IdNonce => idNonce;
+
+ public SessionType SessionType => SessionType.Research;
+
+ Guid? sessionNonce = Guid.NewGuid();
+ public Guid? SessionNonce => sessionNonce;
+
+ public bool Identified => false;
+
+ public AuthenticationMechanism AuthenticationMechanism => AuthenticationMechanism.Unsecured;
+
+ public override string ToString() => UUID;
+ }
+}
+
diff --git a/src/server/API/Controllers/CohortCountController.cs b/src/server/API/Controllers/CohortCountController.cs
index cda84c9f7..c5fdbb2cb 100644
--- a/src/server/API/Controllers/CohortCountController.cs
+++ b/src/server/API/Controllers/CohortCountController.cs
@@ -7,6 +7,9 @@
using System.Threading;
using System.Threading.Tasks;
using API.DTO.Cohort;
+using API.DTO.Integration.Shrine;
+using API.DTO.Integration.Shrine4_1;
+using API.Integration.Shrine4_1;
using Microsoft.AspNetCore.Authorization;
using Microsoft.AspNetCore.Http;
using Microsoft.AspNetCore.Mvc;
@@ -15,10 +18,18 @@
using Model.Cohort;
using Model.Compiler;
using Model.Error;
+using Newtonsoft.Json;
namespace API.Controllers
{
- [Authorize(Policy = TokenType.Access)]
+ public class Test
+ {
+ public string QueryJSON { get; set; }
+ }
+
+ //[Authorize(Policy = TokenType.Access)]
+ [AllowAnonymous]
+ [Produces("application/json")]
[Route("api/cohort/count")]
public class CohortCountController : Controller
{
@@ -29,7 +40,30 @@ public CohortCountController(ILogger logger)
log = logger;
}
- [HttpPost]
+ [HttpPost("shrine")]
+ public async Task> ShrineCount(
+ [FromBody] Test input,
+ [FromServices] ShrineQueryDefinitionConverter queryConverter,
+ [FromServices] CohortCounter counter,
+ CancellationToken cancelToken)
+ {
+ try
+ {
+ var dto = JsonConvert.DeserializeObject(input.QueryJSON);
+ var shrineQuery = dto.ToQuery();
+
+ var query = queryConverter.ToLeafQuery(shrineQuery);
+ var cohort = await counter.Count(query, cancelToken);
+
+ return Ok(cohort.Count.SqlStatements);
+ }
+ catch (Exception ex)
+ {
+ return BadRequest(ex.Message);
+ }
+ }
+
+ [HttpPost]
public async Task> Count(
[FromBody] PatientCountQueryDTO patientCountQuery,
[FromServices] CohortCounter counter,
diff --git a/src/server/API/Controllers/ConfigController.cs b/src/server/API/Controllers/ConfigController.cs
index 50277b017..757d0bf39 100644
--- a/src/server/API/Controllers/ConfigController.cs
+++ b/src/server/API/Controllers/ConfigController.cs
@@ -24,6 +24,7 @@ public class ConfigController : Controller
readonly ClientOptions clientOptions;
readonly AttestationOptions attestationOptions;
readonly DeidentificationOptions deidentOptions;
+ readonly IntegrationOptions integrationOptions;
readonly IServerStateCache serverStateCache;
public ConfigController(
@@ -33,6 +34,7 @@ public ConfigController(
IOptions clientOptions,
IOptions attestationOptions,
IOptions deidentOptions,
+ IOptions integrationOptions,
IServerStateCache serverStateCache)
{
this.authenticationOptions = authenticationOptions.Value;
@@ -41,6 +43,7 @@ public ConfigController(
this.clientOptions = clientOptions.Value;
this.attestationOptions = attestationOptions.Value;
this.deidentOptions = deidentOptions.Value;
+ this.integrationOptions = integrationOptions.Value;
this.serverStateCache = serverStateCache;
}
@@ -112,6 +115,15 @@ public ActionResult Get()
{
Server = versionOptions.Version.ToString(),
Db = serverStateCache.GetServerState().Db.Version.ToString()
+ },
+ Integration = new IntegrationConfigDTO
+ {
+ Enabled = integrationOptions.Enabled,
+ Shrine = integrationOptions.SHRINE != null
+ ? new IntegrationConfigDTO.IntegrationTypeDTO
+ {
+ Enabled = integrationOptions.SHRINE.Enabled
+ } : null
}
};
diff --git a/src/server/API/Controllers/ExportController.cs b/src/server/API/Controllers/ExportController.cs
index 12780782a..2e355ebd2 100644
--- a/src/server/API/Controllers/ExportController.cs
+++ b/src/server/API/Controllers/ExportController.cs
@@ -12,9 +12,7 @@
using Microsoft.Extensions.Logging;
using Microsoft.Extensions.Options;
using Model.Authorization;
-using Model.Export;
using Model.Options;
-using Services.Export;
namespace API.Controllers
{
diff --git a/src/server/API/Controllers/IntegrationController.cs b/src/server/API/Controllers/IntegrationController.cs
new file mode 100644
index 000000000..f5227a800
--- /dev/null
+++ b/src/server/API/Controllers/IntegrationController.cs
@@ -0,0 +1,124 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using System.Threading;
+using API.DTO.Cohort;
+using API.DTO.Integration.Shrine;
+using API.Integration.Shrine;
+using API.Integration.Shrine4_1;
+using Microsoft.AspNetCore.Authorization;
+using Microsoft.AspNetCore.Http;
+using Microsoft.AspNetCore.Mvc;
+using Microsoft.Extensions.Logging;
+using Microsoft.Extensions.Options;
+using Model.Authorization;
+using Model.Integration.Shrine;
+using Model.Options;
+
+namespace API.Controllers
+{
+ [Authorize(Policy = TokenType.Access)]
+ [Authorize(Policy = Access.Institutional)]
+ [Route("api/integration")]
+ public class IntegrationController : Controller
+ {
+ readonly ILogger log;
+ readonly IntegrationOptions opts;
+ readonly ShrineQueryDefinitionConverter converter;
+ readonly IUserContext user;
+ readonly IShrineUserQueryCache userQueryCache;
+ readonly IShrineQueryResultCache queryResultCache;
+ readonly IShrineMessageBroker broker;
+
+ public IntegrationController(
+ ILogger log,
+ IOptions opts,
+ IUserContext user,
+ IShrineUserQueryCache userQueryCache,
+ IShrineQueryResultCache queryResultCache,
+ IShrineMessageBroker broker,
+ ShrineQueryDefinitionConverter converter
+ )
+ {
+ this.log = log;
+ this.opts = opts.Value;
+ this.user = user;
+ this.userQueryCache = userQueryCache;
+ this.queryResultCache = queryResultCache;
+ this.broker = broker;
+ this.converter = converter;
+ }
+
+ [HttpPost("shrine/count")]
+ public ActionResult ShrineCount(
+ [FromBody] PatientCountQueryDTO patientCountQuery
+ )
+ {
+ if (!opts.Enabled || !opts.SHRINE.Enabled) return BadRequest();
+
+ try
+ {
+ var queryId = ShrineQueryDefinitionConverter.GenerateRandomLongId();
+ var queryDefinition = converter.ToShrineQuery(patientCountQuery);
+
+ var researcher = opts.SHRINE.Researcher;
+ var node = opts.SHRINE.Node;
+ var topic = opts.SHRINE.Topic;
+ var runQuery = new ShrineRunQueryForResult
+ {
+ Query = queryDefinition,
+ Researcher = new ShrineResearcher
+ {
+ Id = researcher.Id,
+ VersionInfo = queryDefinition.VersionInfo,
+ UserName = researcher.Name,
+ UserDomainName = researcher.Domain,
+ NodeId = node.Id
+ },
+ Topic = new ShrineTopic
+ {
+ Id = topic.Id,
+ VersionInfo = queryDefinition.VersionInfo,
+ ResearcherId = researcher.Id,
+ Name = topic.Name,
+ Description = topic.Description
+ },
+ ProtocolVersion = 2
+ };
+ var dto = new ShrineRunQueryForResultDTO(runQuery);
+ userQueryCache.Put(queryId, user, patientCountQuery);
+ broker.SendMessageToHub(queryId, dto, ShrineDeliveryContentsType.RunQueryAtHub);
+
+ return Ok(queryId);
+ }
+ catch (Exception ex)
+ {
+ log.LogError("Failed to initialize SHRINE query. Error:{Error}", ex.Message);
+ return StatusCode(StatusCodes.Status500InternalServerError);
+ }
+ }
+
+ [HttpGet("shrine/cohort/{queryId}/count")]
+ public ActionResult GetShrineCountResult(long queryId)
+ {
+ if (!opts.Enabled || !opts.SHRINE.Enabled) return BadRequest();
+
+ try
+ {
+ var results = queryResultCache.GetOrDefault(queryId);
+ if (results == null) return NotFound();
+
+ return Ok(results);
+ }
+ catch (Exception ex)
+ {
+ log.LogError("Failed to retrieve SHRINE query results. Error:{Error}", ex.Message);
+ return StatusCode(StatusCodes.Status500InternalServerError);
+ }
+ }
+ }
+}
+
diff --git a/src/server/API/Controllers/QueryController.cs b/src/server/API/Controllers/QueryController.cs
index 969122b3b..940483473 100644
--- a/src/server/API/Controllers/QueryController.cs
+++ b/src/server/API/Controllers/QueryController.cs
@@ -28,13 +28,11 @@ public class QueryController : Controller
{
readonly ILogger log;
readonly QueryManager manager;
- readonly IUserContext user;
- public QueryController(QueryManager manager, ILogger logger, IUserContext userContext)
+ public QueryController(QueryManager manager, ILogger logger)
{
log = logger;
this.manager = manager;
- user = userContext;
}
[Authorize(Policy = Access.Institutional)]
@@ -81,6 +79,7 @@ public async Task> Get(string ident)
public async Task> Save(
string id,
[FromBody] QuerySaveDTO querySave,
+ [FromServices] IUserContext user,
CancellationToken cancelToken)
{
try
diff --git a/src/server/API/Controllers/UserController.cs b/src/server/API/Controllers/UserController.cs
index 3fed3c070..92c7b2569 100644
--- a/src/server/API/Controllers/UserController.cs
+++ b/src/server/API/Controllers/UserController.cs
@@ -25,27 +25,15 @@ public class UserController : Controller
{
readonly ILogger logger;
readonly AuthenticationOptions authenticationOptions;
- readonly LeafVersionOptions versionOptions;
- readonly CohortOptions cohortOptions;
- readonly ClientOptions clientOptions;
readonly IUserJwtProvider jwtProvider;
- readonly IUserContext userContext;
public UserController(
ILogger logger,
IOptions authenticationOptions,
- IOptions versionOptions,
- IOptions cohortOptions,
- IOptions clientOptions,
- IUserJwtProvider userJwtProvider,
- IUserContext userContext)
+ IUserJwtProvider userJwtProvider)
{
this.logger = logger;
this.authenticationOptions = authenticationOptions.Value;
- this.versionOptions = versionOptions.Value;
- this.cohortOptions = cohortOptions.Value;
- this.clientOptions = clientOptions.Value;
- this.userContext = userContext;
jwtProvider = userJwtProvider;
}
@@ -76,18 +64,20 @@ public async Task> GetUser()
[HttpGet("attest")]
public ActionResult Attest(
[FromQuery] Attestation attestation,
+ [FromServices] IUserContextProvider userContextProvider,
[FromServices] IInvalidatedTokenCache invalidatedCache)
{
- if (authenticationOptions.Mechanism != userContext.AuthenticationMechanism)
+ var user = userContextProvider.GetUserContext();
+ if (authenticationOptions.Mechanism != user.AuthenticationMechanism)
{
return StatusCode(StatusCodes.Status401Unauthorized);
}
try
{
- if (invalidatedCache.IsInvalidated(userContext.IdNonce))
+ if (invalidatedCache.IsInvalidated(user.IdNonce))
{
- logger.LogWarning("Id token is invalidated. IdNonce:{IdNonce} Attestation:{@Attestation}", userContext.IdNonce, attestation);
+ logger.LogWarning("Id token is invalidated. IdNonce:{IdNonce} Attestation:{@Attestation}", user.IdNonce, attestation);
return StatusCode(StatusCodes.Status401Unauthorized);
}
@@ -107,18 +97,21 @@ public ActionResult Attest(
[Authorize(Policy = TokenType.Access)]
[Authorize(Policy = Access.Institutional)]
[HttpGet("refresh")]
- public ActionResult Refresh([FromServices] IInvalidatedTokenCache invalidatedCache)
+ public ActionResult Refresh(
+ [FromServices] IInvalidatedTokenCache invalidatedCache,
+ [FromServices] IUserContextProvider userContextProvider)
{
- if (authenticationOptions.Mechanism != userContext.AuthenticationMechanism)
+ var user = userContextProvider.GetUserContext();
+ if (authenticationOptions.Mechanism != user.AuthenticationMechanism)
{
return StatusCode(StatusCodes.Status401Unauthorized);
}
try
{
- if (invalidatedCache.IsInvalidated(userContext.IdNonce))
+ if (invalidatedCache.IsInvalidated(user.IdNonce))
{
- logger.LogWarning("Id token is invalidated. IdNonce:{IdNonce} Attestation:{@Attestation}", userContext.IdNonce);
+ logger.LogWarning("Id token is invalidated. IdNonce:{IdNonce} Attestation:{@Attestation}", user.IdNonce);
return StatusCode(StatusCodes.Status401Unauthorized);
}
diff --git a/src/server/API/DTO/Config/ConfigDTO.cs b/src/server/API/DTO/Config/ConfigDTO.cs
index 41fec882f..4d0611b73 100644
--- a/src/server/API/DTO/Config/ConfigDTO.cs
+++ b/src/server/API/DTO/Config/ConfigDTO.cs
@@ -15,6 +15,7 @@ public class ConfigDTO
public CohortConfigDTO Cohort { get; set; }
public ClientOptionsDTO Client { get;set; }
public VersionConfigDTO Version { get; set; }
+ public IntegrationConfigDTO Integration { get; set; }
}
public class AuthenticationConfigDTO
@@ -106,4 +107,15 @@ public class VersionConfigDTO
public string Server { get; set; }
public string Db { get; set; }
}
+
+ public class IntegrationConfigDTO
+ {
+ public bool Enabled { get; set; }
+ public IntegrationTypeDTO Shrine { get; set; }
+
+ public class IntegrationTypeDTO
+ {
+ public bool Enabled { get; set; }
+ }
+ }
}
diff --git a/src/server/API/DTO/Integration/Shrine/4_1/ShrineExpressionDTO.cs b/src/server/API/DTO/Integration/Shrine/4_1/ShrineExpressionDTO.cs
new file mode 100644
index 000000000..d69ea47ab
--- /dev/null
+++ b/src/server/API/DTO/Integration/Shrine/4_1/ShrineExpressionDTO.cs
@@ -0,0 +1,337 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using System.Linq;
+using System.Collections.Generic;
+using Model.Compiler;
+using Model.Integration.Shrine4_1;
+
+namespace API.DTO.Integration.Shrine4_1
+{
+ public class ShrineQueryDefinitionDTO
+ {
+ public ShrineConjunctionDTO Expression { get; set; }
+
+ public ShrineQueryDefinitionDTO() { }
+
+ public ShrineQueryDefinitionDTO(ShrineQueryDefinition definition)
+ {
+ Expression = new ShrineConjunctionDTO(definition.Expression);
+ }
+ }
+
+ public class ShrineAnonymousEncodedClassDTO
+ {
+ public string EncodedClass { get; set; }
+
+ public ShrineAnonymousEncodedClassDTO() { }
+
+ public ShrineAnonymousEncodedClassDTO(string encodedClass)
+ {
+ EncodedClass = encodedClass;
+ }
+ }
+
+ public abstract class ShrineGroupDTO : ShrineAnonymousEncodedClassDTO
+ {
+ public int NMustBeTrue { get; set; }
+ public ShrineConjunctionCompareDTO Compare { get; set; }
+
+ public ShrineGroupDTO() { }
+
+ public ShrineGroupDTO(ShrineGroup expr)
+ {
+ NMustBeTrue = expr.NMustBeTrue;
+ Compare = new ShrineConjunctionCompareDTO(expr.Compare);
+ }
+ }
+
+ public class ShrineConjunctionDTO : ShrineAnonymousEncodedClassDTO
+ {
+ public int NMustBeTrue { get; set; }
+ public ShrineConjunctionCompareDTO Compare { get; set; }
+ public IEnumerable Possibilities { get; set; }
+
+ public ShrineConjunctionDTO()
+ {
+ EncodedClass = "Conjunction";
+ }
+
+ public ShrineConjunctionDTO(ShrineConjunction conjunction)
+ {
+ EncodedClass = "Conjunction";
+ Possibilities = conjunction.Possibilities.Select(p => new ShrineConceptGroupOrTimelineDTO(p));
+ }
+ }
+
+ public class ShrineConceptGroupOrTimelineDTO : ShrineConceptGroupDTO
+ {
+ public ShrineConceptGroupDTO First { get; set; }
+ public IEnumerable Subsequent { get; set; } = new List();
+
+ public bool IsConceptGroup => First == null;
+ public bool IsTimeline => First != null;
+
+ public ShrineConceptGroupOrTimelineDTO() { }
+
+ public ShrineConceptGroupOrTimelineDTO(ShrineConceptGroupOrTimeline cg)
+ {
+ if (cg.IsConceptGroup)
+ {
+ Concepts = new ShrineConceptConjunctionDTO(cg.Concepts);
+ EncodedClass = "ConceptGroup";
+ }
+ else
+ {
+ First = new ShrineConceptGroupDTO(cg.First);
+ Subsequent = cg.Subsequent.Select(s => new ShrineTimelineSubsequentEventDTO(s));
+ EncodedClass = "Timeline";
+ }
+ }
+ }
+
+ public class ShrineTimelineSubsequentEventDTO
+ {
+ public ShrineConceptGroupDTO ConceptGroup { get; set; }
+ public ShrineAnonymousEncodedClassDTO PreviousOccurrence { get; set; }
+ public ShrineAnonymousEncodedClassDTO ThisOccurrence { get; set; }
+ public ShrineTimelineSubsequentEventTimeConstraintDTO TimeConstraint { get; set; }
+
+ public ShrineTimelineSubsequentEventDTO() { }
+
+ public ShrineTimelineSubsequentEventDTO(ShrineTimelineSubsequentEvent sub)
+ {
+ ConceptGroup = new ShrineConceptGroupDTO(sub.ConceptGroup);
+ PreviousOccurrence = new ShrineAnonymousEncodedClassDTO(sub.PreviousOccurrence.ToString());
+ ThisOccurrence = new ShrineAnonymousEncodedClassDTO(sub.ThisOccurrence.ToString());
+ TimeConstraint = sub.TimeConstraint != null ? new ShrineTimelineSubsequentEventTimeConstraintDTO(sub.TimeConstraint) : null;
+ }
+ }
+
+ public class ShrineTimelineSubsequentEventTimeConstraintDTO
+ {
+ public ShrineAnonymousEncodedClassDTO Operator { get; set; }
+ public ShrineAnonymousEncodedClassDTO TimeUnit { get; set; }
+ public int Value { get; set; }
+
+ public ShrineTimelineSubsequentEventTimeConstraintDTO() { }
+
+ public ShrineTimelineSubsequentEventTimeConstraintDTO(ShrineTimelineSubsequentEventTimeConstraint timeConstraint)
+ {
+ Operator = new ShrineAnonymousEncodedClassDTO(timeConstraint.Operator.ToString());
+ TimeUnit = new ShrineAnonymousEncodedClassDTO(timeConstraint.TimeUnit.ToString());
+ Value = timeConstraint.Value;
+ }
+ }
+
+ public class ShrineConceptGroupDTO : ShrineGroupDTO
+ {
+ public long? StartDate { get; set; }
+ public long? EndDate { get; set; }
+ public int OccursAtLeast { get; set; } = 1;
+ public ShrineConceptConjunctionDTO Concepts { get; set; }
+
+ public ShrineConceptGroupDTO() { }
+
+ public ShrineConceptGroupDTO(ShrineConceptGroup group) : base(group)
+ {
+ StartDate = group.StartDate != null ? ((DateTimeOffset)group.StartDate).ToUnixTimeMilliseconds() : null;
+ EndDate = group.EndDate != null ? ((DateTimeOffset)group.EndDate).ToUnixTimeMilliseconds() : null;
+ OccursAtLeast = group.OccursAtLeast.HasValue ? (int)group.OccursAtLeast : 1;
+ Concepts = new ShrineConceptConjunctionDTO(group.Concepts);
+ }
+ }
+
+ public class ShrineConceptConjunctionDTO : ShrineAnonymousEncodedClassDTO
+ {
+ public int NMustBeTrue { get; set; }
+ public ShrineConjunctionCompareDTO Compare { get; set; }
+ public IEnumerable Possibilities { get; set; }
+
+ public ShrineConceptConjunctionDTO() { }
+
+ public ShrineConceptConjunctionDTO(ShrineConceptConjunction conjunction)
+ {
+ NMustBeTrue = conjunction.NMustBeTrue;
+ Compare = new ShrineConjunctionCompareDTO(conjunction.Compare);
+ Possibilities = conjunction.Possibilities.Select(p => new ShrineConceptDTO(p));
+ }
+ }
+
+ public class ShrineConceptDTO
+ {
+ public string DisplayName { get; set; }
+ public string TermPath { get; set; }
+ public ShrineConceptConstraintDTO Constraint { get; set; }
+ public static readonly string EncodedClass = "Concept";
+
+ public ShrineConceptDTO() { }
+
+ public ShrineConceptDTO(ShrineConcept concept)
+ {
+ DisplayName = concept.DisplayName;
+ TermPath = concept.TermPath;
+ Constraint = new ShrineConceptConstraintDTO(concept.Constraint);
+ }
+ }
+
+ public class ShrineConceptConstraintDTO
+ {
+ public ShrineAnonymousEncodedClassDTO Operator { get; set; }
+ public decimal? Value { get; set; }
+ public decimal? Value1 { get; set; }
+ public decimal? Value2 { get; set; }
+ public string Unit { get; set; }
+ public string EncodedClass { get; set; }
+
+ public ShrineConceptConstraintDTO() { }
+
+ public ShrineConceptConstraintDTO(ShrineConceptConstraint constraint)
+ {
+ Operator = new ShrineAnonymousEncodedClassDTO { EncodedClass = constraint.Operator.ToString() };
+ Value = constraint.Value;
+ Value1 = constraint.Value1;
+ Value2 = constraint.Value2;
+ Unit = constraint.Unit;
+ }
+ }
+
+ public class ShrineConjunctionCompareDTO : ShrineAnonymousEncodedClassDTO
+ {
+ public ShrineConjunctionCompareDTO() { }
+
+ public ShrineConjunctionCompareDTO(ShrineConjunctionCompare compare)
+ {
+ EncodedClass = compare.EncodedClass.ToString();
+ }
+ }
+
+ public static class ShrineQueryDefinitionExtensions
+ {
+ public static ShrineConjunctionCompare ToCompare(this ShrineConjunctionCompareDTO dto)
+ {
+ _ = Enum.TryParse(dto.EncodedClass, out ShrineConjunctionComparison encodedClass);
+ return new ShrineConjunctionCompare
+ {
+ EncodedClass = encodedClass
+ };
+ }
+
+ public static ShrineConcept ToConcept(this ShrineConceptDTO dto)
+ {
+ return new ShrineConcept
+ {
+ DisplayName = dto.DisplayName,
+ TermPath = dto.TermPath,
+ Constraint = dto.Constraint != null ? dto.Constraint.ToConstraint() : null
+ };
+ }
+
+ public static ShrineConceptConstraint ToConstraint(this ShrineConceptConstraintDTO dto)
+ {
+ NumericFilterType op = NumericFilterType.None;
+ if (dto.Operator != null)
+ {
+ _ = Enum.TryParse(dto.Operator.EncodedClass, out NumericFilterType filterType);
+ op = filterType;
+ }
+ if (op == NumericFilterType.None && dto.Value1.HasValue && dto.Value2.HasValue)
+ {
+ op = NumericFilterType.Between;
+ }
+
+ return new ShrineConceptConstraint
+ {
+ Operator = op,
+ Value = dto.Value,
+ Value1 = dto.Value1,
+ Value2 = dto.Value2,
+ Unit = dto.Unit
+ };
+ }
+
+ public static ShrineConceptGroup ToConceptGroup(this ShrineConceptGroupDTO dto)
+ {
+ return new ShrineConceptGroup
+ {
+ StartDate = dto.StartDate != null ? DateTimeOffset.FromUnixTimeMilliseconds((long)dto.StartDate).UtcDateTime : null,
+ EndDate = dto.EndDate != null ? DateTimeOffset.FromUnixTimeMilliseconds((long)dto.EndDate).UtcDateTime : null,
+ OccursAtLeast = dto.OccursAtLeast,
+ Concepts = dto.Concepts.ToConjunction()
+ };
+ }
+
+ public static ShrineConceptGroupOrTimeline ToConceptGroupOrTimeline(this ShrineConceptGroupOrTimelineDTO dto)
+ {
+ return new ShrineConceptGroupOrTimeline
+ {
+ StartDate = dto.StartDate != null ? DateTimeOffset.FromUnixTimeMilliseconds((long)dto.StartDate).UtcDateTime : null,
+ EndDate = dto.EndDate != null ? DateTimeOffset.FromUnixTimeMilliseconds((long)dto.EndDate).UtcDateTime : null,
+ OccursAtLeast = dto.OccursAtLeast,
+ Concepts = dto.IsConceptGroup ? dto.Concepts.ToConjunction() : null,
+ First = dto.IsTimeline ? dto.First.ToConceptGroup() : null,
+ Subsequent = dto.IsTimeline ? dto.Subsequent.Select(s => s.ToSubsequentEvent()) : null
+ };
+ }
+
+ public static ShrineConjunction ToConjunction(this ShrineConjunctionDTO dto)
+ {
+ return new ShrineConjunction
+ {
+ NMustBeTrue = dto.NMustBeTrue,
+ Compare = dto.Compare.ToCompare(),
+ Possibilities = dto.Possibilities.Select(p => p.ToConceptGroupOrTimeline())
+ };
+ }
+
+ public static ShrineTimelineSubsequentEvent ToSubsequentEvent(this ShrineTimelineSubsequentEventDTO dto)
+ {
+ _ = Enum.TryParse(dto.PreviousOccurrence.EncodedClass, out ShrineOccurrence previousOccurrence);
+ _ = Enum.TryParse(dto.ThisOccurrence.EncodedClass, out ShrineOccurrence thisOccurrence);
+
+ return new ShrineTimelineSubsequentEvent
+ {
+ ConceptGroup = dto.ConceptGroup.ToConceptGroup(),
+ PreviousOccurrence = previousOccurrence,
+ ThisOccurrence = thisOccurrence,
+ TimeConstraint = dto.TimeConstraint != null ? dto.TimeConstraint.ToTimeConstraint() : null
+ };
+ }
+
+ public static ShrineTimelineSubsequentEventTimeConstraint ToTimeConstraint(this ShrineTimelineSubsequentEventTimeConstraintDTO dto)
+ {
+ _ = Enum.TryParse(dto.Operator.EncodedClass, out NumericFilterType op);
+ _ = Enum.TryParse(dto.TimeUnit.EncodedClass, out DateIncrementType timeUnit);
+
+ return new ShrineTimelineSubsequentEventTimeConstraint
+ {
+ Operator = op,
+ TimeUnit = timeUnit,
+ Value = dto.Value
+ };
+ }
+
+ public static ShrineConceptConjunction ToConjunction(this ShrineConceptConjunctionDTO dto)
+ {
+ return new ShrineConceptConjunction
+ {
+ NMustBeTrue = dto.NMustBeTrue,
+ Compare = dto.Compare.ToCompare(),
+ Possibilities = dto.Possibilities.Select(p => p.ToConcept())
+ };
+ }
+
+
+ public static ShrineQueryDefinition ToDefinition(this ShrineQueryDefinitionDTO dto)
+ {
+ return new ShrineQueryDefinition
+ {
+ Expression = dto.Expression.ToConjunction()
+ };
+ }
+ }
+}
+
diff --git a/src/server/API/DTO/Integration/Shrine/4_1/ShrineQueryDTO.cs b/src/server/API/DTO/Integration/Shrine/4_1/ShrineQueryDTO.cs
new file mode 100644
index 000000000..a210fd221
--- /dev/null
+++ b/src/server/API/DTO/Integration/Shrine/4_1/ShrineQueryDTO.cs
@@ -0,0 +1,75 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using API.DTO.Integration.Shrine;
+using Model.Integration.Shrine4_1;
+
+namespace API.DTO.Integration.Shrine4_1
+{
+ public class ShrineQueryDTO
+ {
+ public long Id { get; set; }
+ public ShrineVersionInfoDTO VersionInfo { get; set; }
+ public ShrineQueryDefinitionDTO QueryDefinition { get; set; }
+ public ShrineAnonymousEncodedClassDTO Output { get; set; }
+ public ShrineAnonymousEncodedClassDTO Status { get; set; }
+ public string QueryName { get; set; }
+ public long NodeOfOriginId { get; set; }
+ public long ResearcherId { get; set; }
+ public long TopicId { get; set; }
+ public string ProjectName { get; set; }
+ public bool Flagged { get; set; }
+ public string FlaggedMessage { get; set; }
+ public string EncodedClass { get; set; }
+
+ public ShrineQueryDTO() { }
+
+ public ShrineQueryDTO(ShrineQuery query)
+ {
+ Id = query.Id;
+ VersionInfo = new ShrineVersionInfoDTO(query.VersionInfo);
+ QueryDefinition = new ShrineQueryDefinitionDTO(query.QueryDefinition);
+ Status = new ShrineAnonymousEncodedClassDTO(query.Status.ToString());
+ Output = new ShrineAnonymousEncodedClassDTO(query.Output.ToString());
+ QueryName = query.QueryName;
+ NodeOfOriginId = query.NodeOfOriginId;
+ ResearcherId = query.ResearcherId;
+ TopicId = query.TopicId;
+ ProjectName = query.ProjectName;
+ Flagged = query.Flagged;
+ FlaggedMessage = query.FlaggedMessage;
+ EncodedClass = query?.EncodedClass.ToString();
+ }
+ }
+
+ public static class ShrineQueryExtensions
+ {
+ public static ShrineQuery ToQuery(this ShrineQueryDTO dto)
+ {
+ _ = Enum.TryParse(dto?.EncodedClass, out ShrineQueryType type);
+ _ = Enum.TryParse(dto?.Status?.EncodedClass, out ShrineStatusType status);
+ _ = Enum.TryParse(dto?.Output?.EncodedClass, out ShrineOutputType output);
+
+ return new ShrineQuery
+ {
+ Id = dto.Id,
+ VersionInfo = dto?.VersionInfo?.ToVersionInfo(),
+ Status = status,
+ QueryDefinition = dto.QueryDefinition.ToDefinition(),
+ Output = output,
+ QueryName = dto?.QueryName,
+ NodeOfOriginId = dto.NodeOfOriginId,
+ ResearcherId = dto.ResearcherId,
+ TopicId = dto.TopicId,
+ ProjectName = dto.ProjectName,
+ Flagged = dto.Flagged,
+ FlaggedMessage = dto.FlaggedMessage,
+ EncodedClass = type
+ };
+ }
+ }
+}
+
diff --git a/src/server/API/DTO/Integration/Shrine/ShrineDeliveryAttemptDTO.cs b/src/server/API/DTO/Integration/Shrine/ShrineDeliveryAttemptDTO.cs
new file mode 100644
index 000000000..216b52e24
--- /dev/null
+++ b/src/server/API/DTO/Integration/Shrine/ShrineDeliveryAttemptDTO.cs
@@ -0,0 +1,74 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using Model.Integration.Shrine;
+
+namespace API.DTO.Integration.Shrine
+{
+ public class ShrineDeliveryAttemptDTO
+ {
+ public ShrineInnerDeliveryAttemptDTO DeliveryAttemptId { get; set; } = new ShrineInnerDeliveryAttemptDTO();
+ public long MillisecondsToComplete { get; set; }
+ public int RemainingAttempts { get; set; }
+ public string Contents { get; set; }
+
+ public ShrineDeliveryAttemptDTO() { }
+ }
+
+ public class ShrineInnerDeliveryAttemptDTO
+ {
+ public long Underlying { get; set; }
+ }
+
+ public class ShrineDeliveryContentsDTO
+ {
+ public string Contents { get; set; }
+ public long ContentsSubject { get; set; }
+ public string ContentsType { get; set; }
+ public int ProtocolVersion = 2;
+
+ public ShrineDeliveryContentsDTO() { }
+
+ public ShrineDeliveryContentsDTO(ShrineDeliveryContents contents)
+ {
+ Contents = contents.Contents;
+ ContentsSubject = contents.ContentsSubject;
+ ContentsType = contents.ContentsType.ToString();
+ }
+ }
+
+ public static class ShrineDeliveryExtensions
+ {
+ public static ShrineDeliveryAttempt ToDeliveryAttempt(this ShrineDeliveryAttemptDTO dto)
+ {
+ if (dto == null) return null;
+ return new ShrineDeliveryAttempt
+ {
+ DeliveryAttemptId = new ShrineInnerDeliveryAttempt
+ {
+ Underlying = dto.DeliveryAttemptId.Underlying
+ },
+ MillisecondsToComplete = dto.MillisecondsToComplete,
+ RemainingAttempts = dto.RemainingAttempts,
+ Contents = dto.Contents
+ };
+ }
+
+ public static ShrineDeliveryContents ToContents(this ShrineDeliveryContentsDTO dto)
+ {
+ if (dto == null) return null;
+ _ = Enum.TryParse(dto.ContentsType, out ShrineDeliveryContentsType contentsType);
+
+ return new ShrineDeliveryContents
+ {
+ Contents = dto.Contents,
+ ContentsSubject = dto.ContentsSubject,
+ ContentsType = contentsType
+ };
+ }
+ }
+}
+
diff --git a/src/server/API/DTO/Integration/Shrine/ShrineNodeDTO.cs b/src/server/API/DTO/Integration/Shrine/ShrineNodeDTO.cs
new file mode 100644
index 000000000..92f50ac3f
--- /dev/null
+++ b/src/server/API/DTO/Integration/Shrine/ShrineNodeDTO.cs
@@ -0,0 +1,66 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using Model.Integration.Shrine;
+
+namespace API.DTO.Integration.Shrine
+{
+ public class ShrineNodeDTO
+ {
+ public long Id { get; set; }
+ public ShrineVersionInfoDTO VersionInfo { get; set; }
+ public string Name { get; set; }
+ public string Key { get; set; }
+ public string UserDomainName { get; set; }
+ public string MomQueueName { get; set; }
+ public string AdminEmail { get; set; }
+ public bool SendQueries { get; set; }
+ public int UnderstandsProtocol { get; set; }
+ public string MomId { get; set; }
+
+ public ShrineNodeDTO()
+ {
+
+ }
+
+ public ShrineNodeDTO(ShrineNode node)
+ {
+ Id = node.Id;
+ VersionInfo = new ShrineVersionInfoDTO(node.VersionInfo);
+ Name = node.Name;
+ Key = node.Key;
+ UserDomainName = node.UserDomainName;
+ MomQueueName = node.MomQueueName;
+ AdminEmail = node.AdminEmail;
+ SendQueries = node.SendQueries;
+ UnderstandsProtocol = node.UnderstandsProtocol;
+ MomId = node.MomId;
+ }
+ }
+
+ public static class ShrineNodeExtensions
+ {
+ public static ShrineNode ToNode(this ShrineNodeDTO dto)
+ {
+ if (dto == null) return null;
+
+ return new ShrineNode
+ {
+ Id = dto.Id,
+ VersionInfo = dto.VersionInfo.ToVersionInfo(),
+ Name = dto.Name,
+ Key = dto.Key,
+ UserDomainName = dto.UserDomainName,
+ MomQueueName = dto.MomQueueName,
+ AdminEmail = dto.AdminEmail,
+ SendQueries = dto.SendQueries,
+ UnderstandsProtocol = dto.UnderstandsProtocol,
+ MomId = dto.MomId
+ };
+ }
+ }
+}
+
diff --git a/src/server/API/DTO/Integration/Shrine/ShrineQueryStatusDTO.cs b/src/server/API/DTO/Integration/Shrine/ShrineQueryStatusDTO.cs
new file mode 100644
index 000000000..c93577761
--- /dev/null
+++ b/src/server/API/DTO/Integration/Shrine/ShrineQueryStatusDTO.cs
@@ -0,0 +1,35 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using Model.Integration.Shrine;
+
+namespace API.DTO.Integration.Shrine
+{
+ public class ShrineQueryStatusDTO
+ {
+ public string EncodedClass { get; set; }
+
+ public ShrineQueryStatusDTO() { }
+
+ public ShrineQueryStatusDTO(ShrineQueryStatus status)
+ {
+ EncodedClass = status.EncodedClass.ToString();
+ }
+ }
+
+ public static class ShrineQueryStatusExtensions
+ {
+ public static ShrineQueryStatus ToStatus(this ShrineQueryStatusDTO dto)
+ {
+ _ = Enum.TryParse(dto.EncodedClass, out ShrineQueryStatusType type);
+ return new ShrineQueryStatus
+ {
+ EncodedClass = type
+ };
+ }
+ }
+}
+
diff --git a/src/server/API/DTO/Integration/Shrine/ShrineResearcherDTO.cs b/src/server/API/DTO/Integration/Shrine/ShrineResearcherDTO.cs
new file mode 100644
index 000000000..8e93391a0
--- /dev/null
+++ b/src/server/API/DTO/Integration/Shrine/ShrineResearcherDTO.cs
@@ -0,0 +1,50 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using Model.Integration.Shrine;
+
+namespace API.DTO.Integration.Shrine
+{
+ public class ShrineResearcherDTO
+ {
+ public long Id { get; set; }
+ public ShrineVersionInfoDTO VersionInfo { get; set; }
+ public string UserName { get; set; }
+ public string UserDomainName { get; set; }
+ public long NodeId { get; set; }
+
+ public ShrineResearcherDTO()
+ {
+
+ }
+
+ public ShrineResearcherDTO(ShrineResearcher researcher)
+ {
+ Id = researcher.Id;
+ VersionInfo = new ShrineVersionInfoDTO(researcher.VersionInfo);
+ UserName = researcher.UserName;
+ UserDomainName = researcher.UserDomainName;
+ NodeId = researcher.NodeId;
+ }
+ }
+
+ public static class ShrineResearcherExtensions
+ {
+ public static ShrineResearcher ToReseacher(this ShrineResearcherDTO dto)
+ {
+ if (dto == null) return null;
+ return new ShrineResearcher
+ {
+ Id = dto.Id,
+ VersionInfo = dto.VersionInfo.ToVersionInfo(),
+ UserName = dto.UserName,
+ UserDomainName = dto.UserDomainName,
+ NodeId = dto.NodeId
+ };
+ }
+ }
+}
+
diff --git a/src/server/API/DTO/Integration/Shrine/ShrineResultProgressDTO.cs b/src/server/API/DTO/Integration/Shrine/ShrineResultProgressDTO.cs
new file mode 100644
index 000000000..098b05912
--- /dev/null
+++ b/src/server/API/DTO/Integration/Shrine/ShrineResultProgressDTO.cs
@@ -0,0 +1,95 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using Model.Integration.Shrine;
+
+namespace API.DTO.Integration.Shrine
+{
+ public class ShrineResultProgressDTO
+ {
+ public long Id { get; set; }
+ public ShrineVersionInfoDTO VersionInfo { get; set; }
+ public long QueryId { get; set; }
+ public long AdapterNodeId { get; set; }
+ public string AdapterNodeName { get; set; }
+ public ShrineQueryStatusDTO Status { get; set; }
+ public string StatusMessage { get; set; }
+ public long? CrcQueryInstanceId { get; set; }
+ public string EncodedClass { get; set; }
+ public int? Count { get; set; }
+ public ShrineResultObfuscatingParametersDTO ObfuscatingParameters { get; set; }
+
+ public ShrineResultProgressDTO() { }
+
+ public ShrineResultProgressDTO(ShrineResultProgress progress)
+ {
+ Id = progress.Id;
+ VersionInfo = new ShrineVersionInfoDTO(progress.VersionInfo);
+ QueryId = progress.QueryId;
+ AdapterNodeId = progress.AdapterNodeId;
+ AdapterNodeName = progress.AdapterNodeName;
+ Status = new ShrineQueryStatusDTO(progress.Status);
+ StatusMessage = progress.StatusMessage;
+ CrcQueryInstanceId = progress?.CrcQueryInstanceId;
+ EncodedClass = progress.EncodedClass.ToString();
+ Count = progress?.Count;
+ ObfuscatingParameters = new ShrineResultObfuscatingParametersDTO(progress.ObfuscatingParameters);
+ }
+ }
+
+ public class ShrineResultObfuscatingParametersDTO
+ {
+ public int BinSize { get; set; }
+ public decimal StdDev { get; set; }
+ public int NoiseClamp { get; set; }
+ public int LowLimit { get; set; }
+
+ public ShrineResultObfuscatingParametersDTO(ShrineResultObfuscatingParameters parameters)
+ {
+ if (parameters == null) return;
+ BinSize = parameters.BinSize;
+ StdDev = parameters.StdDev;
+ NoiseClamp = parameters.NoiseClamp;
+ LowLimit = parameters.LowLimit;
+ }
+ }
+
+ public static class ShrineResultProgressExtensions
+ {
+ public static ShrineResultProgress ToProgress(this ShrineResultProgressDTO dto)
+ {
+ _ = Enum.TryParse(dto.EncodedClass, out ShrineQueryStatusType type);
+
+ return new ShrineResultProgress
+ {
+ Id = dto.Id,
+ VersionInfo = dto.VersionInfo.ToVersionInfo(),
+ QueryId = dto.QueryId,
+ AdapterNodeId = dto.AdapterNodeId,
+ AdapterNodeName = dto.AdapterNodeName,
+ Status = dto.Status.ToStatus(),
+ StatusMessage = dto.StatusMessage,
+ CrcQueryInstanceId = dto.CrcQueryInstanceId,
+ Count = dto.Count ?? -1,
+ ObfuscatingParameters = dto.ObfuscatingParameters?.ToParameters(),
+ EncodedClass = type
+ };
+ }
+
+ public static ShrineResultObfuscatingParameters ToParameters(this ShrineResultObfuscatingParametersDTO dto)
+ {
+ if (dto == null) return null;
+ return new ShrineResultObfuscatingParameters
+ {
+ BinSize = dto.BinSize,
+ StdDev = dto.StdDev,
+ NoiseClamp = dto.NoiseClamp,
+ LowLimit = dto.LowLimit
+ };
+ }
+ }
+}
+
diff --git a/src/server/API/DTO/Integration/Shrine/ShrineRunQueryForResultDTO.cs b/src/server/API/DTO/Integration/Shrine/ShrineRunQueryForResultDTO.cs
new file mode 100644
index 000000000..a17e70b10
--- /dev/null
+++ b/src/server/API/DTO/Integration/Shrine/ShrineRunQueryForResultDTO.cs
@@ -0,0 +1,53 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using API.DTO.Integration.Shrine4_1;
+using Model.Integration.Shrine;
+
+namespace API.DTO.Integration.Shrine
+{
+ public class ShrineRunQueryForResultDTO
+ {
+ public ShrineQueryDTO Query { get; set; }
+ public ShrineNodeDTO Node { get; set; }
+ public ShrineTopicDTO Topic { get; set; }
+ public ShrineResultProgressDTO ResultProgress { get; set; }
+ public ShrineResearcherDTO Researcher { get; set; }
+ public int ProtocolVersion { get; set; }
+
+ public ShrineRunQueryForResultDTO()
+ {
+
+ }
+
+ public ShrineRunQueryForResultDTO(ShrineRunQueryForResult runQueryForResult)
+ {
+ Query = new ShrineQueryDTO(runQueryForResult.Query);
+ Node = runQueryForResult.Node != null ? new ShrineNodeDTO(runQueryForResult.Node) : null;
+ Topic = runQueryForResult.Topic != null ? new ShrineTopicDTO(runQueryForResult.Topic) : null;
+ ResultProgress = runQueryForResult.ResultProgress != null ? new ShrineResultProgressDTO(runQueryForResult.ResultProgress) : null;
+ Researcher = runQueryForResult.Researcher != null ? new ShrineResearcherDTO(runQueryForResult.Researcher) : null;
+ ProtocolVersion = runQueryForResult.ProtocolVersion;
+ }
+ }
+
+ public static class ShrineRunQueryForResultExtensions
+ {
+ public static ShrineRunQueryForResult ToRunQueryForResult(this ShrineRunQueryForResultDTO dto)
+ {
+ if (dto == null) return null;
+ return new ShrineRunQueryForResult
+ {
+ Query = dto?.Query.ToQuery(),
+ Node = dto?.Node.ToNode(),
+ Topic = dto?.Topic.ToTopic(),
+ ResultProgress = dto?.ResultProgress.ToProgress(),
+ Researcher = dto?.Researcher.ToReseacher()
+ };
+ }
+ }
+}
+
diff --git a/src/server/API/DTO/Integration/Shrine/ShrineTopicDTO.cs b/src/server/API/DTO/Integration/Shrine/ShrineTopicDTO.cs
new file mode 100644
index 000000000..577862503
--- /dev/null
+++ b/src/server/API/DTO/Integration/Shrine/ShrineTopicDTO.cs
@@ -0,0 +1,50 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using Model.Integration.Shrine;
+
+namespace API.DTO.Integration.Shrine
+{
+ public class ShrineTopicDTO
+ {
+ public long Id { get; set; }
+ public ShrineVersionInfoDTO VersionInfo { get; set; }
+ public long ResearcherId { get; set; }
+ public string Name { get; set; }
+ public string Description { get; set; }
+
+ public ShrineTopicDTO()
+ {
+
+ }
+
+ public ShrineTopicDTO(ShrineTopic topic)
+ {
+ Id = topic.Id;
+ VersionInfo = new ShrineVersionInfoDTO(topic.VersionInfo);
+ ResearcherId = topic.ResearcherId;
+ Name = topic.Name;
+ Description = topic.Description;
+ }
+ }
+
+ public static class ShrineTopicExtensions
+ {
+ public static ShrineTopic ToTopic(this ShrineTopicDTO dto)
+ {
+ if (dto == null) return null;
+ return new ShrineTopic
+ {
+ Id = dto.Id,
+ VersionInfo = dto.VersionInfo.ToVersionInfo(),
+ ResearcherId = dto.ResearcherId,
+ Name = dto.Name,
+ Description = dto.Description
+ };
+ }
+ }
+}
+
diff --git a/src/server/API/DTO/Integration/Shrine/ShrineUpdateQueryAtQepDTO.cs b/src/server/API/DTO/Integration/Shrine/ShrineUpdateQueryAtQepDTO.cs
new file mode 100644
index 000000000..917cde49f
--- /dev/null
+++ b/src/server/API/DTO/Integration/Shrine/ShrineUpdateQueryAtQepDTO.cs
@@ -0,0 +1,60 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using System.Linq;
+using System.Collections.Generic;
+using Model.Integration.Shrine;
+
+namespace API.DTO.Integration.Shrine
+{
+ public class ShrineUpdateQueryAtQepDTO
+ {
+ public long QueryId { get; set; }
+ public ShrineQueryStatusDTO QueryStatus { get; set; }
+ public long ChangeDate { get; set; }
+ public string EncodedClass { get; set; }
+ public IEnumerable ResultProgresses { get; set; }
+
+ public ShrineUpdateQueryAtQepDTO() { }
+
+ public ShrineUpdateQueryAtQepDTO(ShrineUpdateQueryAtQep update)
+ {
+ QueryId = update.QueryId;
+ QueryStatus = new ShrineQueryStatusDTO(update.QueryStatus);
+ ChangeDate = ((DateTimeOffset)update.ChangeDate).ToUnixTimeMilliseconds();
+ EncodedClass = update.EncodedClass.ToString();
+
+ if (update.ResultProgresses != null)
+ {
+ ResultProgresses = update.ResultProgresses.Select(p => new ShrineResultProgressDTO(p));
+ }
+ }
+ }
+
+ public static class ShrineUpdateQueryAtQepExtensions
+ {
+ public static ShrineUpdateQueryAtQep ToUpdate(this ShrineUpdateQueryAtQepDTO dto)
+ {
+ _ = Enum.TryParse(dto.EncodedClass, out ShrineQueryStatusType type);
+
+ var output = new ShrineUpdateQueryAtQep
+ {
+ QueryId = dto.QueryId,
+ QueryStatus = dto.QueryStatus.ToStatus(),
+ ChangeDate = DateTimeOffset.FromUnixTimeMilliseconds(dto.ChangeDate).UtcDateTime,
+ EncodedClass = type
+ };
+
+ if (dto.ResultProgresses != null)
+ {
+ output.ResultProgresses = dto.ResultProgresses.Select(p => p.ToProgress());
+ }
+
+ return output;
+ }
+ }
+}
+
diff --git a/src/server/API/DTO/Integration/Shrine/ShrineUpdateResultWithCrcResultDTO.cs b/src/server/API/DTO/Integration/Shrine/ShrineUpdateResultWithCrcResultDTO.cs
new file mode 100644
index 000000000..ab2c9f3b2
--- /dev/null
+++ b/src/server/API/DTO/Integration/Shrine/ShrineUpdateResultWithCrcResultDTO.cs
@@ -0,0 +1,67 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using Model.Integration.Shrine;
+
+namespace API.DTO.Integration.Shrine
+{
+ public class ShrineUpdateResultWithCrcResultDTO : ShrineUpdateResultWithProgressDTO
+ {
+ public ShrineBreakdownDTO Breakdowns { get; set; }
+ public ShrineResultObfuscatingParametersDTO ObfuscatingParameters { get; set; }
+ public int Count { get; set; }
+
+ public ShrineUpdateResultWithCrcResultDTO(ShrineUpdateResultWithCrcResult update) : base(update)
+ {
+ ObfuscatingParameters = new ShrineResultObfuscatingParametersDTO(update.ObfuscatingParameters);
+ Count = update.Count;
+ if (update.Breakdowns != null)
+ {
+ Breakdowns = new ShrineBreakdownDTO(update.Breakdowns);
+ }
+ }
+ }
+
+ public class ShrineBreakdownDTO
+ {
+ public object[] Counts { get; set; }
+
+ public ShrineBreakdownDTO(ShrineBreakdown breakdown)
+ {
+ Counts = breakdown.Counts;
+ }
+ }
+
+ public static class ShrineUpdateResultWithCrcResultDTOExtensions
+ {
+ public static ShrineUpdateResultWithCrcResult ToUpdate(this ShrineUpdateResultWithCrcResultDTO dto)
+ {
+ _ = Enum.TryParse(dto.EncodedClass, out ShrineQueryStatusType type);
+
+ var output = new ShrineUpdateResultWithCrcResult
+ {
+ QueryId = dto.QueryId,
+ AdapterNodeKey = dto.AdapterNodeKey,
+ Status = dto.Status.ToStatus(),
+ StatusMessage = dto.StatusMessage,
+ CrcQueryInstanceId = dto.CrcQueryInstanceId,
+ AdapterTime = DateTimeOffset.FromUnixTimeMilliseconds(dto.AdapterTime).UtcDateTime,
+ EncodedClass = type,
+ ObfuscatingParameters = dto.ObfuscatingParameters.ToParameters(),
+ Count = dto.Count,
+ Breakdowns = dto?.Breakdowns.ToBreakdown()
+ };
+
+ return output;
+ }
+
+ public static ShrineBreakdown ToBreakdown(this ShrineBreakdownDTO dto)
+ {
+ return new ShrineBreakdown { Counts = dto.Counts };
+ }
+ }
+}
+
diff --git a/src/server/API/DTO/Integration/Shrine/ShrineUpdateResultWithProgressDTO.cs b/src/server/API/DTO/Integration/Shrine/ShrineUpdateResultWithProgressDTO.cs
new file mode 100644
index 000000000..bbe104d4a
--- /dev/null
+++ b/src/server/API/DTO/Integration/Shrine/ShrineUpdateResultWithProgressDTO.cs
@@ -0,0 +1,54 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using Model.Integration.Shrine;
+
+namespace API.DTO.Integration.Shrine
+{
+ public class ShrineUpdateResultWithProgressDTO
+ {
+ public long QueryId { get; set; }
+ public string AdapterNodeKey { get; set; }
+ public ShrineQueryStatusDTO Status { get; set; }
+ public string StatusMessage { get; set; }
+ public long? CrcQueryInstanceId { get; set; }
+ public long AdapterTime { get; set; }
+ public string EncodedClass { get; set; }
+
+ public ShrineUpdateResultWithProgressDTO(ShrineUpdateResultWithProgress update)
+ {
+ QueryId = update.QueryId;
+ AdapterNodeKey = update.AdapterNodeKey;
+ Status = new ShrineQueryStatusDTO(update.Status);
+ StatusMessage = update.StatusMessage;
+ CrcQueryInstanceId = update.CrcQueryInstanceId;
+ AdapterTime = ((DateTimeOffset)update.AdapterTime).ToUnixTimeMilliseconds();
+ EncodedClass = update.EncodedClass.ToString();
+ }
+ }
+
+ public static class ShrineUpdateResultWithProgressDTOExtensions
+ {
+ public static ShrineUpdateResultWithProgress ToUpdate(this ShrineUpdateResultWithProgressDTO dto)
+ {
+ _ = Enum.TryParse(dto.EncodedClass, out ShrineQueryStatusType type);
+
+ var output = new ShrineUpdateResultWithProgress
+ {
+ QueryId = dto.QueryId,
+ AdapterNodeKey = dto.AdapterNodeKey,
+ Status = dto.Status.ToStatus(),
+ StatusMessage = dto.StatusMessage,
+ CrcQueryInstanceId = dto.CrcQueryInstanceId,
+ AdapterTime = DateTimeOffset.FromUnixTimeMilliseconds(dto.AdapterTime).UtcDateTime,
+ EncodedClass = type
+ };
+
+ return output;
+ }
+ }
+}
+
diff --git a/src/server/API/DTO/Integration/Shrine/ShrineVersionInfoDTO.cs b/src/server/API/DTO/Integration/Shrine/ShrineVersionInfoDTO.cs
new file mode 100644
index 000000000..7c0b4aacc
--- /dev/null
+++ b/src/server/API/DTO/Integration/Shrine/ShrineVersionInfoDTO.cs
@@ -0,0 +1,48 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using Model.Integration.Shrine;
+
+namespace API.DTO.Integration.Shrine
+{
+ public class ShrineVersionInfoDTO
+ {
+ public int ProtocolVersion { get; set; }
+ public int ItemVersion { get; set; }
+ public string ShrineVersion { get; set; }
+ public long CreateDate { get; set; }
+ public long ChangeDate { get; set; }
+
+ public ShrineVersionInfoDTO() { }
+
+ public ShrineVersionInfoDTO(ShrineVersionInfo ver)
+ {
+ if (ver == null) return;
+
+ ProtocolVersion = ver.ProtocolVersion;
+ ItemVersion = ver.ItemVersion;
+ ShrineVersion = ver.ShrineVersion;
+ CreateDate = ((DateTimeOffset)ver.CreateDate).ToUnixTimeMilliseconds();
+ ChangeDate = ((DateTimeOffset)ver.ChangeDate).ToUnixTimeMilliseconds();
+ }
+ }
+
+ public static class ShrineVersionInfoExtensions
+ {
+ public static ShrineVersionInfo ToVersionInfo(this ShrineVersionInfoDTO dto)
+ {
+ return new ShrineVersionInfo
+ {
+ ProtocolVersion = dto.ProtocolVersion,
+ ItemVersion = dto.ItemVersion,
+ ShrineVersion = dto.ShrineVersion,
+ CreateDate = DateTimeOffset.FromUnixTimeMilliseconds(dto.CreateDate).UtcDateTime,
+ ChangeDate = DateTimeOffset.FromUnixTimeMilliseconds(dto.ChangeDate).UtcDateTime
+ };
+ }
+ }
+}
+
diff --git a/src/server/API/GlobalSuppressions.cs b/src/server/API/GlobalSuppressions.cs
new file mode 100644
index 000000000..eb011dc41
--- /dev/null
+++ b/src/server/API/GlobalSuppressions.cs
@@ -0,0 +1,8 @@
+// This file is used by Code Analysis to maintain SuppressMessage
+// attributes that are applied to this project.
+// Project-level suppressions either have no target or are given
+// a specific target and scoped to a namespace, type, member, etc.
+
+using System.Diagnostics.CodeAnalysis;
+
+[assembly: SuppressMessage("Naming", "CA1707:Identifiers should not contain underscores", Justification = "", Scope = "namespace", Target = "~N:API.DTO.Integration.Shrine4_1")]
diff --git a/src/server/API/Integration/Shrine/4_1/ShrineDemographicsConverter.cs b/src/server/API/Integration/Shrine/4_1/ShrineDemographicsConverter.cs
new file mode 100644
index 000000000..413310704
--- /dev/null
+++ b/src/server/API/Integration/Shrine/4_1/ShrineDemographicsConverter.cs
@@ -0,0 +1,92 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using System.Linq;
+using Model.Cohort;
+using Model.Integration.Shrine;
+
+namespace API.Integration.Shrine4_1
+{
+ public class ShrineDemographicsConverter
+ {
+ public ShrineBreakdown ToShrineBreakdown(DemographicProvider.Result result)
+ {
+ var stats = result.Demographics.Statistics;
+ var leafGenders = stats.BinarySplitData.Where(bs => bs.Category == "Gender").First();
+ var leafVitals = stats.BinarySplitData.Where(bs => bs.Category == "VitalStatus").First();
+ var leafRaces = stats.NihRaceEthnicityData.EthnicBackgrounds;
+ var leafAges = stats.AgeByGenderData.Buckets;
+
+ object[][] gender =
+ {
+ new object[] { "Female", leafGenders.Left.Value },
+ new object[] { "Male", leafGenders.Right.Value },
+ new object[] { "Unknown", -1 }
+ };
+
+ object[][] races = leafRaces.Select(r =>
+ {
+ var h = r.Value.Hispanic;
+ var n = r.Value.NotHispanic;
+ var u = r.Value.Unknown;
+ var sum = h.Females + h.Males + h.Others + n.Females + n.Males + n.Others + u.Females + u.Males + u.Others;
+ return new object[] { Capitalize(r.Key), sum };
+ }).ToArray();
+
+ object[][] vitals =
+ {
+ new object[] { "Living", leafVitals.Left.Value },
+ new object[] { "Deceased", leafVitals.Right.Value },
+ new object[] { "Deferred", -1 },
+ new object[] { "Not recorded", -1 }
+ };
+
+ // SHRINE uses slightly different age buckets, but we can avoid recalculating everything
+ var zero = leafAges.Where(a => a.Key == "<1" || a.Key == "1-9").Sum(a => a.Value.Females + a.Value.Males + a.Value.Others);
+ var ten = leafAges.Where(a => a.Key == "10-17").Sum(a => a.Value.Females + a.Value.Males + a.Value.Others);
+ var eighteen = leafAges.Where(a => a.Key == "18-24" || a.Key == "25-34").Sum(a => a.Value.Females + a.Value.Males + a.Value.Others);
+ var thirtyfive = leafAges.Where(a => a.Key == "35-44").Sum(a => a.Value.Females + a.Value.Males + a.Value.Others);
+ var fortyfive = leafAges.Where(a => a.Key == "45-54").Sum(a => a.Value.Females + a.Value.Males + a.Value.Others);
+ var fiftyfive = leafAges.Where(a => a.Key == "55-64").Sum(a => a.Value.Females + a.Value.Males + a.Value.Others);
+ var sixtyfive = leafAges.Where(a => a.Key == "65-74").Sum(a => a.Value.Females + a.Value.Males + a.Value.Others);
+ var seventyfive = leafAges.Where(a => a.Key == "75-84").Sum(a => a.Value.Females + a.Value.Males + a.Value.Others);
+ var eightyfive = leafAges.Where(a => a.Key == ">84").Sum(a => a.Value.Females + a.Value.Males + a.Value.Others);
+ var sixtyfiveplus = sixtyfive + seventyfive + eightyfive;
+
+ object[][] ages =
+ {
+ // Note: the spaces are not a typo. SHRINE (I assume unintentionally?) has spaces before buckets,
+ // so we have to match them to get viz to line up
+ new object[] { " 0-9 years old", NegativeOneIfZero(zero) },
+ new object[] { " 10-17 years old", NegativeOneIfZero(ten) },
+ new object[] { " 18-34 years old", NegativeOneIfZero(eighteen) },
+ new object[] { " 35-44 years old", NegativeOneIfZero(thirtyfive) },
+ new object[] { " 45-54 years old", NegativeOneIfZero(fortyfive) },
+ new object[] { " 55-64 years old", NegativeOneIfZero(fiftyfive) },
+ new object[] { " 65-74 years old", NegativeOneIfZero(sixtyfive) },
+ new object[] { " 75-84 years old", NegativeOneIfZero(seventyfive) },
+ new object[] { ">= 65 years old", NegativeOneIfZero(sixtyfiveplus) },
+ new object[] { ">= 85 years old", NegativeOneIfZero(eightyfive) }
+ };
+
+ return new ShrineBreakdown
+ {
+ Counts = new object[]
+ {
+ new object[] { "PATIENT_GENDER_COUNT_XML", gender },
+ new object[] { "PATIENT_RACE_COUNT_XML", races },
+ new object[] { "PATIENT_VITALSTATUS_COUNT_XML", vitals },
+ new object[] { "PATIENT_AGE_COUNT_XML", ages },
+ }
+ };
+ }
+
+ static int NegativeOneIfZero(int value) => value == 0 ? -1 : value;
+
+ static string Capitalize(string text) => char.ToUpper(text[0]) + text.Remove(0, 1);
+ }
+}
+
diff --git a/src/server/API/Integration/Shrine/4_1/ShrineQueryDefinitionConverter.cs b/src/server/API/Integration/Shrine/4_1/ShrineQueryDefinitionConverter.cs
new file mode 100644
index 000000000..e3afbbe68
--- /dev/null
+++ b/src/server/API/Integration/Shrine/4_1/ShrineQueryDefinitionConverter.cs
@@ -0,0 +1,324 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using API.DTO.Cohort;
+using API.DTO.Compiler;
+using Microsoft.Extensions.Options;
+using Model.Compiler;
+using Model.Integration.Shrine;
+using Model.Integration.Shrine4_1;
+using Model.Options;
+
+namespace API.Integration.Shrine4_1
+{
+ public class ShrineQueryDefinitionConverter
+ {
+ readonly string UniversalIdPrefix = $"urn:leaf:concept:shrine:";
+ readonly ShrineIntegrationOptions opts;
+
+ public ShrineQueryDefinitionConverter(IOptions opts)
+ {
+ this.opts = opts.Value;
+ }
+
+ public IPatientCountQueryDTO ToLeafQuery(ShrineQuery shrineQuery)
+ {
+ var possibilities = shrineQuery.QueryDefinition.Expression.Possibilities;
+ var panels = possibilities.Select((grp, i) => grp.IsConceptGroup
+ ? ShrineConceptGroupToPanelDTO(grp, i)
+ : ShrineTimelineToPanelDTO(grp, i)
+ );
+
+ return new PatientCountQueryDTO
+ {
+ QueryId = Guid.NewGuid().ToString(),
+ Panels = panels,
+ PanelFilters = Array.Empty()
+ };
+ }
+
+ PanelDTO ShrineConceptGroupToPanelDTO(ShrineConceptGroup conceptGroup, int i)
+ {
+ return new PanelDTO
+ {
+ IncludePanel = conceptGroup.Concepts.NMustBeTrue > 0,
+ Index = i,
+ Domain = PanelDomain.Panel,
+ DateFilter = conceptGroup.StartDate.HasValue || conceptGroup.EndDate.HasValue ?
+ new DateBoundary
+ {
+ Start = new DateFilter { Date = conceptGroup.StartDate ?? new DateTime(1900, 1, 1), DateIncrementType = DateIncrementType.Specific },
+ End = new DateFilter { Date = conceptGroup.EndDate ?? DateTime.Now, DateIncrementType = DateIncrementType.Specific }
+ }
+ : null,
+ SubPanels = new List
+ {
+ new SubPanelDTO
+ {
+ IncludeSubPanel = true,
+ Index = 0,
+ MinimumCount = conceptGroup.OccursAtLeast.HasValue ? (int)conceptGroup.OccursAtLeast : 1,
+ PanelIndex = i,
+ PanelItems = conceptGroup.Concepts.Possibilities.Select((c,j) =>
+ {
+ return new PanelItemDTO
+ {
+ Index = j,
+ SubPanelIndex = 0,
+ PanelIndex = i,
+ NumericFilter = c?.Constraint != null && c?.Constraint?.Operator != NumericFilterType.None
+ ? new NumericFilter
+ {
+ FilterType = c.Constraint.Operator,
+ Filter = c.Constraint.Value.HasValue
+ ? new decimal[] { (decimal)c.Constraint.Value }
+ : new decimal[] { (decimal)c.Constraint.Value1, (decimal)c.Constraint.Value2 }
+ }
+ : null,
+ Resource = new ResourceRef
+ {
+ UiDisplayName = c.DisplayName,
+ UniversalId = UniversalIdPrefix + c.TermPath
+ }
+ };
+ })
+ }
+ }
+ };
+ }
+
+ PanelDTO ShrineTimelineToPanelDTO(ShrineConceptGroupOrTimeline timeline, int i)
+ {
+ var first = new SubPanelDTO
+ {
+ IncludeSubPanel = timeline.First.Concepts.NMustBeTrue > 0,
+ Index = 0,
+ MinimumCount = timeline.First.Concepts.NMustBeTrue,
+ PanelIndex = i,
+ PanelItems = timeline.First.Concepts.Possibilities.Select((c, j) =>
+ {
+ return new PanelItemDTO
+ {
+ Index = j,
+ SubPanelIndex = 0,
+ PanelIndex = i,
+ RecencyFilter = timeline.Subsequent.First().PreviousOccurrence == ShrineOccurrence.First
+ ? RecencyFilterType.Min
+ : RecencyFilterType.None,
+ NumericFilter = c?.Constraint != null && c?.Constraint?.Operator != NumericFilterType.None
+ ? new NumericFilter
+ {
+ FilterType = c.Constraint.Operator,
+ Filter = c.Constraint.Value.HasValue
+ ? new decimal[] { (decimal)c.Constraint.Value }
+ : new decimal[] { (decimal)c.Constraint.Value1, (decimal)c.Constraint.Value2 }
+ }
+ : null,
+ Resource = new ResourceRef
+ {
+ UiDisplayName = c.DisplayName,
+ UniversalId = UniversalIdPrefix + c.TermPath
+ }
+ };
+ })
+ };
+
+ var subsequent = timeline.Subsequent.Select((sub, i) =>
+ {
+ return new SubPanelDTO
+ {
+ IncludeSubPanel = sub.ConceptGroup.NMustBeTrue > 0,
+ Index = i + 1,
+ MinimumCount = (int)sub.ConceptGroup.OccursAtLeast,
+ JoinSequence = new SubPanelJoinSequence
+ {
+ Increment = sub.TimeConstraint != null ? sub.TimeConstraint.Value : -1,
+ DateIncrementType = sub.TimeConstraint != null ? sub.TimeConstraint.TimeUnit : DateIncrementType.None,
+ SequenceType = SequenceType.AnytimeFollowing
+ },
+ PanelIndex = i,
+ PanelItems = sub.ConceptGroup.Concepts.Possibilities.Select((c, j) =>
+ {
+ return new PanelItemDTO
+ {
+ Index = j,
+ SubPanelIndex = 0,
+ PanelIndex = i,
+ RecencyFilter = sub.ThisOccurrence == ShrineOccurrence.First
+ ? RecencyFilterType.Min
+ : RecencyFilterType.None,
+ NumericFilter = c?.Constraint != null && c?.Constraint?.Operator != NumericFilterType.None
+ ? new NumericFilter
+ {
+ FilterType = c.Constraint.Operator,
+ Filter = c.Constraint.Value.HasValue
+ ? new decimal[] { (decimal)c.Constraint.Value }
+ : new decimal[] { (decimal)c.Constraint.Value1, (decimal)c.Constraint.Value2 }
+ }
+ : null,
+ Resource = new ResourceRef
+ {
+ UiDisplayName = c.DisplayName,
+ UniversalId = UniversalIdPrefix + c.TermPath
+ }
+ };
+ })
+ };
+ });
+
+ return new PanelDTO
+ {
+ IncludePanel = timeline.First.Concepts.NMustBeTrue > 0,
+ Index = i,
+ Domain = PanelDomain.Panel,
+ DateFilter = timeline.StartDate.HasValue ?
+ new DateBoundary
+ {
+ Start = new DateFilter { Date = timeline.StartDate.Value },
+ End = new DateFilter { Date = timeline.EndDate.Value }
+ }
+ : null,
+ SubPanels = new List() { first }.Union(subsequent)
+ };
+ }
+
+ public ShrineQuery ToShrineQuery(IPatientCountQueryDTO leafQuery)
+ {
+ var panels = leafQuery.All();
+
+ return new ShrineQuery
+ {
+ Id = GenerateRandomLongId(),
+ VersionInfo = new ShrineVersionInfo
+ {
+ ProtocolVersion = 2,
+ ShrineVersion = "4.1.0-SNAPSHOT",
+ ItemVersion = 2,
+ CreateDate = DateTime.Now,
+ ChangeDate = DateTime.Now
+ },
+ Status = ShrineStatusType.SentToHub,
+ QueryDefinition = new ShrineQueryDefinition
+ {
+ Expression = new ShrineConjunction
+ {
+ NMustBeTrue = panels.Count(),
+ Compare = new ShrineConjunctionCompare
+ {
+ EncodedClass = ShrineConjunctionComparison.AtLeast
+ },
+ Possibilities = panels.Select(p =>
+ {
+ return p.SubPanels.Count() > 1 && p.SubPanels.ElementAt(1).PanelItems.Any()
+ ? LeafNonSequenceToShrineConceptGroup(p)
+ : LeafSequenceToShrineTimeline(p);
+ })
+ }
+ },
+ Output = ShrineOutputType.Count,
+ QueryName = "Query"
+ };
+ }
+
+ ShrineConceptGroupOrTimeline LeafNonSequenceToShrineConceptGroup(IPanelDTO panel)
+ {
+ var subpanel = panel.SubPanels.First();
+
+ return new ShrineConceptGroupOrTimeline
+ {
+ Concepts = LeafSubPanelToShrineConceptConjunction(panel, subpanel)
+ };
+ }
+
+ ShrineConceptGroupOrTimeline LeafSequenceToShrineTimeline(IPanelDTO panel)
+ {
+ var firstSubpanel = panel.SubPanels.First();
+ var first = new ShrineConceptGroup
+ {
+ Concepts = LeafSubPanelToShrineConceptConjunction(panel, firstSubpanel)
+ };
+
+ var subsequent = panel.SubPanels.Skip(1).Select(subpanel =>
+ {
+ return new ShrineTimelineSubsequentEvent
+ {
+ ConceptGroup = new ShrineConceptGroup
+ {
+ Concepts = LeafSubPanelToShrineConceptConjunction(panel, subpanel)
+ },
+ PreviousOccurrence = ShrineOccurrence.Any,
+ ThisOccurrence = ShrineOccurrence.Any,
+ TimeConstraint = subpanel.JoinSequence.SequenceType == SequenceType.WithinFollowing
+ ? new ShrineTimelineSubsequentEventTimeConstraint
+ {
+ Operator = NumericFilterType.LessThanOrEqual,
+ TimeUnit = subpanel.JoinSequence.DateIncrementType,
+ Value = subpanel.JoinSequence.Increment
+ }
+ : null
+ };
+ });
+
+ return new ShrineConceptGroupOrTimeline
+ {
+ First = first,
+ Subsequent = subsequent
+ };
+ }
+
+ ShrineConceptConjunction LeafSubPanelToShrineConceptConjunction(IPanelDTO panel, ISubPanelDTO subpanel)
+ {
+ return new ShrineConceptConjunction
+ {
+ NMustBeTrue = panel.IncludePanel ? 1 : 0,
+ Compare = new ShrineConjunctionCompare
+ {
+ EncodedClass = panel.IncludePanel ? ShrineConjunctionComparison.AtLeast : ShrineConjunctionComparison.AtMost,
+ },
+ Possibilities = subpanel.PanelItems.Select(pi =>
+ {
+ return new ShrineConcept
+ {
+ DisplayName = pi.Resource.UiDisplayName,
+ TermPath = pi.Resource.UniversalId.ToString().Replace(UniversalIdPrefix, ""),
+ Constraint = pi.NumericFilter != null && pi.NumericFilter.FilterType != NumericFilterType.None
+ ? new ShrineConceptConstraint
+ {
+ Operator = pi.NumericFilter.FilterType,
+ Value = pi.NumericFilter.FilterType != NumericFilterType.Between ? pi.NumericFilter.Filter.First() : null,
+ Value1 = pi.NumericFilter.FilterType == NumericFilterType.Between ? pi.NumericFilter.Filter.First() : null,
+ Value2 = pi.NumericFilter.FilterType == NumericFilterType.Between ? pi.NumericFilter.Filter.Last() : null
+ }
+ : null
+ };
+ }),
+ StartDate = panel.DateFilter?.Start?.Date,
+ EndDate = panel.DateFilter?.End?.Date,
+ OccursAtLeast = panel.IncludePanel ? subpanel.MinimumCount : 0
+ };
+ }
+
+ public static long GenerateRandomLongId()
+ {
+ //return LongRandom(10000000000000000, long.MaxValue, new Random());
+ Random random = new();
+ byte[] bytes = new byte[8];
+ random.NextBytes(bytes);
+ return BitConverter.ToInt64(bytes, 0);
+ }
+
+ static long LongRandom(long min, long max, Random rand)
+ {
+ long result = rand.Next((int)(min >> 32), (int)(max >> 32));
+ result <<= 32;
+ result |= (long)rand.Next((int)min, (int)max);
+ return result;
+ }
+ }
+}
+
diff --git a/src/server/API/Integration/Shrine/ShrineMessageBroker.cs b/src/server/API/Integration/Shrine/ShrineMessageBroker.cs
new file mode 100644
index 000000000..71360cd69
--- /dev/null
+++ b/src/server/API/Integration/Shrine/ShrineMessageBroker.cs
@@ -0,0 +1,107 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using System.Net.Http;
+using System.Text;
+using System.Threading.Tasks;
+using API.DTO.Integration.Shrine;
+using Microsoft.Extensions.Options;
+using Model.Integration.Shrine;
+using Model.Options;
+using Newtonsoft.Json;
+using Newtonsoft.Json.Serialization;
+
+namespace API.Integration.Shrine
+{
+ public interface IShrineMessageBroker
+ {
+ Task<(HttpResponseMessage, ShrineDeliveryContents)> ReadHubMessageAndAcknowledge();
+ Task SendMessageToHub(ShrineDeliveryContents contents);
+ Task SendMessageToHub(long queryId, object contents, ShrineDeliveryContentsType type);
+ }
+
+ public class ShrineMessageBroker : IShrineMessageBroker
+ {
+ readonly HttpClient client;
+ readonly ShrineIntegrationOptions opts;
+ readonly int TimeOutSeconds = 5;
+ readonly JsonSerializerSettings serializerSettings = new JsonSerializerSettings
+ {
+ ContractResolver = new CamelCasePropertyNamesContractResolver()
+ };
+
+ public ShrineMessageBroker(HttpClient client, IOptions opts)
+ {
+ this.client = client;
+ this.opts = opts.Value.SHRINE;
+ }
+
+ public async Task<(HttpResponseMessage, ShrineDeliveryContents)> ReadHubMessageAndAcknowledge()
+ {
+ var req = new HttpRequestMessage
+ {
+ RequestUri = new Uri($"{opts.HubApiURI}/shrine-api/mom/receiveMessage/{opts.Node.Name}?timeOutSeconds={TimeOutSeconds}"),
+ Method = HttpMethod.Get
+ };
+
+ var resp = await client.SendAsync(req);
+ req.Dispose();
+ if (!resp.IsSuccessStatusCode || resp.Content == null)
+ {
+ return (resp, null);
+ }
+
+ var jsonMessage = await resp.Content.ReadAsStringAsync();
+ if (string.IsNullOrEmpty(jsonMessage))
+ {
+ return (resp, null);
+ }
+ var message = JsonConvert.DeserializeObject(jsonMessage).ToDeliveryAttempt();
+
+ var ack = new HttpRequestMessage
+ {
+ RequestUri = new Uri($"{opts.HubApiURI}/shrine-api/mom/acknowledge/{message.DeliveryAttemptId.Underlying}"),
+ Method = HttpMethod.Put
+ };
+ _ = await client.SendAsync(ack);
+ ack.Dispose();
+
+ var contents = JsonConvert.DeserializeObject(message.Contents);
+
+ return (resp, contents.ToContents());
+ }
+
+ public async Task SendMessageToHub(long queryId, object contents, ShrineDeliveryContentsType type)
+ {
+ var delivery = new ShrineDeliveryContents
+ {
+ ContentsSubject = queryId,
+ Contents = JsonConvert.SerializeObject(contents, serializerSettings),
+ ContentsType = type
+ };
+ return await SendMessageToHub(delivery);
+ }
+
+ public async Task SendMessageToHub(ShrineDeliveryContents contents)
+ {
+ var request = new HttpRequestMessage
+ {
+ RequestUri = new Uri($"{opts.HubApiURI}/shrine-api/mom/sendMessage/hub"),
+ Method = HttpMethod.Put,
+ Content = new StringContent(
+ JsonConvert.SerializeObject(new ShrineDeliveryContentsDTO(contents), serializerSettings),
+ Encoding.UTF8,
+ "application/x-www-form-urlencoded"
+ )
+ };
+ var response = await client.SendAsync(request);
+ request.Dispose();
+
+ return response;
+ }
+ }
+}
+
diff --git a/src/server/API/Jobs/BackgroundShrineCacheSynchronizer.cs b/src/server/API/Jobs/BackgroundShrineCacheSynchronizer.cs
new file mode 100644
index 000000000..82f338f7f
--- /dev/null
+++ b/src/server/API/Jobs/BackgroundShrineCacheSynchronizer.cs
@@ -0,0 +1,68 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using Microsoft.Extensions.Hosting;
+using Microsoft.Extensions.Logging;
+using Model.Integration.Shrine;
+using System.Threading;
+using System.Threading.Tasks;
+
+namespace API.Jobs
+{
+ public class BackgroundShrineCacheSynchronizer : BackgroundService
+ {
+ readonly ILogger logger;
+ readonly IShrineQueryResultCache queryResultCache;
+ readonly IShrineUserQueryCache userQueryCache;
+ readonly int cacheDeleteFrequencyMinutes = 60;
+
+ DateTime? lastCacheDelete;
+
+ public BackgroundShrineCacheSynchronizer(
+ ILogger logger,
+ IShrineQueryResultCache queryResultCache,
+ IShrineUserQueryCache userQueryCache)
+ {
+ this.logger = logger;
+ this.queryResultCache = queryResultCache;
+ this.userQueryCache = userQueryCache;
+ }
+
+ protected override async Task ExecuteAsync(CancellationToken stoppingToken)
+ {
+ logger.LogInformation("BackgroundShrineCacheSynchronizer is starting");
+
+ stoppingToken.Register(() =>
+ {
+ logger.LogInformation("BackgroundShrineCacheSynchronizer is stopped");
+ });
+
+ while (!stoppingToken.IsCancellationRequested)
+ {
+ try
+ {
+ if (lastCacheDelete == null) continue;
+ logger.LogInformation($"BackgroundShrineCacheSynchronizer will delete old cached records older than {cacheDeleteFrequencyMinutes} minutes");
+
+ var resultCount = queryResultCache.DeleteOlderThan((DateTime)lastCacheDelete);
+ var queryCount = userQueryCache.DeleteOlderThan((DateTime)lastCacheDelete);
+ lastCacheDelete = DateTime.Now;
+
+ logger.LogInformation("BackgroundShrineCacheSynchronizer deleted {resultCount} results and {queryCount} queries", resultCount, queryCount);
+ }
+ catch (Exception ex)
+ {
+ logger.LogError("BackgroundShrineCacheSynchronizer failed to clear caches. Error: {Error}", ex.ToString());
+ }
+ finally
+ {
+ await Task.Delay(TimeSpan.FromMinutes(cacheDeleteFrequencyMinutes));
+ }
+ }
+ }
+ }
+}
+
diff --git a/src/server/API/Jobs/BackgroundShrinePollingService.cs b/src/server/API/Jobs/BackgroundShrinePollingService.cs
new file mode 100644
index 000000000..6386e9806
--- /dev/null
+++ b/src/server/API/Jobs/BackgroundShrinePollingService.cs
@@ -0,0 +1,296 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using System.Threading;
+using System.Threading.Tasks;
+using API.DTO.Integration.Shrine;
+using API.DTO.Cohort;
+using API.Authorization;
+using API.Integration.Shrine;
+using API.Integration.Shrine4_1;
+using Microsoft.Extensions.DependencyInjection;
+using Microsoft.Extensions.Hosting;
+using Microsoft.Extensions.Logging;
+using Model.Authorization;
+using Model.Cohort;
+using Model.Integration.Shrine;
+using Newtonsoft.Json;
+using Model.Compiler;
+using Model.Options;
+using Microsoft.Extensions.Options;
+
+namespace API.Jobs
+{
+ public class BackgroundShrinePollingService : BackgroundService
+ {
+ readonly ILogger logger;
+ readonly IShrineMessageBroker broker;
+ readonly IShrineQueryResultCache queryResultCache;
+ readonly IShrineUserQueryCache userQueryCache;
+ readonly IServiceScopeFactory serviceScopeFactory;
+ readonly DeidentificationOptions deidentOpts;
+ readonly ShrineIntegrationOptions opts;
+ readonly ShrineQueryDefinitionConverter queryConverter;
+ readonly ShrineDemographicsConverter demographicsConverter;
+ readonly int ErrorPauseSeconds = 300;
+
+ public BackgroundShrinePollingService(
+ ILogger logger,
+ IShrineMessageBroker broker,
+ IShrineQueryResultCache queryResultCache,
+ IShrineUserQueryCache userQueryCache,
+ IServiceScopeFactory serviceScopeFactory,
+ IOptions deidentOpts,
+ IOptions opts,
+ ShrineQueryDefinitionConverter queryConverter,
+ ShrineDemographicsConverter demographicsConverter
+ )
+ {
+ this.logger = logger;
+ this.broker = broker;
+ this.queryResultCache = queryResultCache;
+ this.userQueryCache = userQueryCache;
+ this.serviceScopeFactory = serviceScopeFactory;
+ this.queryConverter = queryConverter;
+ this.demographicsConverter = demographicsConverter;
+ this.opts = opts.Value.SHRINE;
+ this.deidentOpts = deidentOpts.Value;
+ }
+
+ protected override async Task ExecuteAsync(CancellationToken stoppingToken)
+ {
+ logger.LogInformation("BackgroundShrinePollingService is starting");
+
+ stoppingToken.Register(() =>
+ {
+ logger.LogInformation("BackgroundShrinePollingService is stopped");
+ });
+
+ while (!stoppingToken.IsCancellationRequested)
+ {
+ try
+ {
+ var (response, message) = await broker.ReadHubMessageAndAcknowledge();
+ if (message == null)
+ {
+ if (!response.IsSuccessStatusCode)
+ {
+ // Error, delay before next poll
+ await Task.Delay(TimeSpan.FromSeconds(ErrorPauseSeconds), stoppingToken);
+ }
+ continue;
+ }
+
+ _ = Task.Run(async () =>
+ {
+ switch (message.ContentsType)
+ {
+ case ShrineDeliveryContentsType.UpdateQueryAtQep:
+ var update = JsonConvert.DeserializeObject(message.Contents).ToUpdate();
+ HandleUpdateQueryAtQepMessage(update);
+ break;
+
+ case ShrineDeliveryContentsType.RunQueryForResult:
+ try
+ {
+ var dto = JsonConvert.DeserializeObject(message.Contents);
+ var run = dto.ToRunQueryForResult();
+ await HandleRunQueryForResultMessage(run, stoppingToken);
+ }
+ catch (JsonSerializationException ex)
+ {
+ logger.LogError("BackgroundShrinePollingService failed to parse SHRINE message. Error: {Error}", ex.ToString());
+ }
+ catch (Exception ex)
+ {
+ logger.LogError("BackgroundShrinePollingService encountered an error. Error: {Error}", ex.ToString());
+ }
+ break;
+
+ case ShrineDeliveryContentsType.Result:
+ var result = JsonConvert.DeserializeObject(message.Contents).ToProgress();
+ HandleResultMessage(result);
+ break;
+
+ default:
+ break;
+ }
+ }, stoppingToken);
+ }
+ catch (JsonSerializationException e)
+ {
+ logger.LogError("BackgroundShrinePollingService failed to parse SHRINE message. Error: {Error}", e.ToString());
+ }
+ catch (Exception e)
+ {
+ logger.LogError("BackgroundShrinePollingService failed to synchronize with SHRINE. Error: {Error}", e.ToString());
+ logger.LogInformation($"BackgroundShrinePollingService pausing {ErrorPauseSeconds} seconds.");
+ await Task.Delay(TimeSpan.FromSeconds(ErrorPauseSeconds), stoppingToken);
+ }
+ }
+
+ logger.LogInformation("BackgroundShrinePollingService is stopped");
+ }
+
+ void HandleUpdateQueryAtQepMessage(ShrineUpdateQueryAtQep update)
+ {
+ if (update.ResultProgresses != null)
+ {
+ queryResultCache.Put(update.ToQueryResult());
+ }
+ }
+
+ void HandleResultMessage(ShrineResultProgress progress)
+ {
+ queryResultCache.Put(progress);
+ }
+
+ async Task HandleRunQueryForResultMessage(ShrineRunQueryForResult run, CancellationToken stoppingToken)
+ {
+ // Let hub know query received
+ await SendQueryReceievedByAdapter(run.Query.Id);
+
+ // Get user context, convert query
+ var (user, query) = GetContext(run);
+
+ // Let hub know query converted, executing
+ await SendQuerySubmittedToCrc(run.Query.Id);
+
+ // Query conversion failed, tell hub no patients
+ if (query == null)
+ {
+ await SendFailedQueryResult(run.Query.Id);
+ return;
+ }
+
+ // Create scope to ensure query run as this user
+ using (var scope = serviceScopeFactory.CreateAsyncScope())
+ {
+ var userContextProvider = scope.ServiceProvider.GetRequiredService();
+ userContextProvider.SetUserContext(user);
+ var counter = scope.ServiceProvider.GetRequiredService();
+
+ var cohort = await counter.Count(query, stoppingToken);
+ var count = new CohortCountDTO(cohort);
+
+ if (!cohort.ValidationContext.PreflightPassed)
+ {
+ await SendFailedQueryResult(run.Query.Id);
+ return;
+ }
+
+ queryResultCache.Put(run.Query.Id, run.Researcher);
+
+ // Check if we need to get demographics as well
+ if (run.Query.Output == Model.Integration.Shrine4_1.ShrineOutputType.DemographicsAndCount)
+ {
+ var queryRef = new QueryRef(count.QueryId);
+ var demographicsProvider = scope.ServiceProvider.GetRequiredService();
+ var demographics = await demographicsProvider.GetDemographicsAsync(queryRef, stoppingToken);
+ var breakdowns = demographicsConverter.ToShrineBreakdown(demographics);
+
+ // Let hub know demographics result
+ await SendQueryResult(run.Query.Id, count.Result.Value, breakdowns);
+ }
+ else
+ {
+ // Let hub know query result
+ await SendQueryResult(run.Query.Id, count.Result.Value);
+ }
+ }
+ }
+
+ async Task SendFailedQueryResult(long queryId)
+ {
+ await SendQueryResult(queryId, -1);
+ }
+
+ async Task SendQueryResult(long queryId, int count)
+ {
+ await SendQueryResult(queryId, count, null);
+ }
+
+ async Task SendQueryResult(long queryId, int count, ShrineBreakdown breakdowns)
+ {
+ var message = new ShrineUpdateResultWithCrcResult
+ {
+ QueryId = queryId,
+ AdapterNodeKey = opts.Node.Key,
+ Count = count,
+ CrcQueryInstanceId = 42,
+ Breakdowns = breakdowns,
+ ObfuscatingParameters = new ShrineResultObfuscatingParameters
+ {
+ BinSize = 5,
+ StdDev = 6.5M,
+ NoiseClamp = deidentOpts.Cohort.Enabled && deidentOpts.Cohort.Noise.Enabled
+ ? Math.Max(deidentOpts.Cohort.Noise.LowerBound, deidentOpts.Cohort.Noise.UpperBound)
+ : 10,
+ LowLimit = deidentOpts.Cohort.Enabled && deidentOpts.Cohort.LowCellSizeMasking.Enabled
+ ? deidentOpts.Cohort.LowCellSizeMasking.Threshold
+ : 10
+ },
+ Status = new ShrineQueryStatus { EncodedClass = ShrineQueryStatusType.ResultFromCRC },
+ StatusMessage = "FINISHED",
+ AdapterTime = DateTime.Now,
+ EncodedClass = ShrineQueryStatusType.UpdateResultWithCrcResult
+ };
+ var dto = new ShrineUpdateResultWithCrcResultDTO(message);
+
+ _ = await broker.SendMessageToHub(queryId, dto, ShrineDeliveryContentsType.UpdateResult);
+ }
+
+ async Task SendQueryReceievedByAdapter(long queryId)
+ {
+ await SendQueryReceivedMessage(queryId, ShrineQueryStatusType.ReceivedByAdapter, ShrineQueryStatusType.UpdateResultWithProgress);
+ }
+
+ async Task SendQuerySubmittedToCrc(long queryId)
+ {
+ await SendQueryReceivedMessage(queryId, ShrineQueryStatusType.SubmittedToCRC, ShrineQueryStatusType.UpdateResultWithProgress);
+ }
+
+ async Task SendQueryReceivedMessage(long queryId, ShrineQueryStatusType innerClass, ShrineQueryStatusType outerClass)
+ {
+ var message = new ShrineUpdateResultWithProgress
+ {
+ QueryId = queryId,
+ AdapterNodeKey = opts.Node.Key,
+ Status = new ShrineQueryStatus { EncodedClass = innerClass },
+ AdapterTime = DateTime.Now,
+ EncodedClass = outerClass
+ };
+ var dto = new ShrineUpdateResultWithProgressDTO(message);
+
+ _ = await broker.SendMessageToHub(queryId, dto, ShrineDeliveryContentsType.UpdateResult);
+ }
+
+ (IUserContext, IPatientCountQueryDTO) GetContext(ShrineRunQueryForResult run)
+ {
+ var cached = userQueryCache.GetOrDefault(run.Query.Id);
+
+ // If run by a Leaf user, grab from cache
+ if (cached != null)
+ {
+ return (cached.User, cached.Query);
+ }
+
+ // Else not from Leaf, so set user context and transform query defintion
+ IPatientCountQueryDTO query = null;
+ try
+ {
+ query = queryConverter.ToLeafQuery(run.Query);
+ }
+ catch (Exception ex)
+ {
+ logger.LogError("Failed to convert SHRINE query to Leaf query. SHRINE query: {@Query}. Error: {Error}", run.Query, ex.ToString());
+ }
+
+ return (new ShrineUserContext(run.Researcher), query);
+ }
+ }
+}
+
diff --git a/src/server/API/Middleware/Federation/RejectInvalidFederatedUserMiddleware.cs b/src/server/API/Middleware/Federation/RejectInvalidFederatedUserMiddleware.cs
index f9362e1c9..2e3d50a8e 100644
--- a/src/server/API/Middleware/Federation/RejectInvalidFederatedUserMiddleware.cs
+++ b/src/server/API/Middleware/Federation/RejectInvalidFederatedUserMiddleware.cs
@@ -15,9 +15,9 @@ public class RejectInvalidFederatedUserMiddleware : IMiddleware
readonly IUserContext user;
readonly ILogger logger;
- public RejectInvalidFederatedUserMiddleware(IUserContext userContext, ILogger logger)
+ public RejectInvalidFederatedUserMiddleware(IUserContext user, ILogger logger)
{
- this.user = userContext;
+ this.user = user;
this.logger = logger;
}
diff --git a/src/server/API/Options/Config.Integration.cs b/src/server/API/Options/Config.Integration.cs
new file mode 100644
index 000000000..3dd78dd38
--- /dev/null
+++ b/src/server/API/Options/Config.Integration.cs
@@ -0,0 +1,45 @@
+// Copyright (c) 2022, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+
+namespace API.Options
+{
+ public static partial class Config
+ {
+ public static class Integration
+ {
+ public const string Enabled = @"Integration:Enabled";
+
+ public static class SHRINE
+ {
+ public const string Section = @"Integration:SHRINE";
+ public const string Enabled = @"Integration:SHRINE:Enabled";
+ public const string HubApiURI = @"Integration:SHRINE:HubApiURI";
+
+ public static class Node
+ {
+ public const string Id = @"Integration:SHRINE:Node:Id";
+ public const string Key = @"Integration:SHRINE:Node:Key";
+ public const string Name = @"Integration:SHRINE:Node:Name";
+ }
+
+ public static class Researcher
+ {
+ public const string Id = @"Integration:SHRINE:Researcher:Id";
+ public const string Name = @"Integration:SHRINE:Researcher:Name";
+ public const string Domain = @"Integration:SHRINE:Researcher:Domain";
+ }
+
+ public static class Topic
+ {
+ public const string Id = @"Integration:SHRINE:Topic:Id";
+ public const string Name = @"Integration:SHRINE:Topic:Name";
+ public const string Description = @"Integration:SHRINE:Topic:Description";
+ }
+ }
+ }
+ }
+}
diff --git a/src/server/API/Options/StartupExtensions.Options.cs b/src/server/API/Options/StartupExtensions.Options.cs
index 2b69d0de9..0ff3f28d8 100644
--- a/src/server/API/Options/StartupExtensions.Options.cs
+++ b/src/server/API/Options/StartupExtensions.Options.cs
@@ -50,6 +50,9 @@ public static IServiceCollection ConfigureLeafOptions(
// Import Options
services.ConfigureImportOptions(configuration);
+ // Integrations Options
+ services.ConfigureIntegrationOptions(configuration);
+
// Authentication Options
services.ConfigureAuthenticationOptions(configuration);
@@ -251,6 +254,50 @@ static IServiceCollection ConfigureImportOptions(this IServiceCollection service
return services;
}
+ static IServiceCollection ConfigureIntegrationOptions(this IServiceCollection services, IConfiguration config)
+ {
+ var enabled = config.GetValue(Config.Integration.Enabled);
+
+ if (enabled)
+ {
+ config.TryGetValue(Config.Integration.SHRINE.Enabled, out bool shrineEnabled);
+ if (shrineEnabled)
+ {
+ var shrine = new ShrineIntegrationOptions
+ {
+ Enabled = shrineEnabled,
+ HubApiURI = config.GetValue(Config.Integration.SHRINE.HubApiURI),
+ Node = new ShrineIntegrationOptions.LocalNode
+ {
+ Id = config.GetValue(Config.Integration.SHRINE.Node.Id),
+ Key = config.GetValue(Config.Integration.SHRINE.Node.Key),
+ Name = config.GetValue(Config.Integration.SHRINE.Node.Name)
+ },
+ Researcher = new ShrineIntegrationOptions.LocalResearcher
+ {
+ Id = config.GetValue(Config.Integration.SHRINE.Researcher.Id),
+ Name = config.GetValue(Config.Integration.SHRINE.Researcher.Name),
+ Domain = config.GetValue(Config.Integration.SHRINE.Researcher.Domain)
+ },
+ Topic = new ShrineIntegrationOptions.DefaultTopic
+ {
+ Id = config.GetValue(Config.Integration.SHRINE.Topic.Id),
+ Name = config.GetValue(Config.Integration.SHRINE.Topic.Name),
+ Description = config.GetValue(Config.Integration.SHRINE.Topic.Description)
+ }
+ };
+
+ services.Configure(opts =>
+ {
+ opts.Enabled = true;
+ opts.SHRINE = shrine;
+ });
+ }
+ }
+
+ return services;
+ }
+
static IServiceCollection ConfigureClientOptions(this IServiceCollection services, IConfiguration config)
{
services.Configure(opts =>
@@ -412,14 +459,15 @@ static IServiceCollection ConfigureCompilerOptions(this IServiceCollection servi
// App Db Connection
services.Configure(opts =>
{
- opts.ConnectionString = config.GetByProxy(Config.Db.App.Connection);
+ opts.ConnectionString = "Server=localhost,1432;Database=LeafDB;uid=sa;Password=Jefferson407!;"; //config.GetByProxy(Config.Db.App.Connection);
+ //opts.ConnectionString = config.GetByProxy(Config.Db.App.Connection);
opts.DefaultTimeout = config.GetValue(Config.Db.App.DefaultTimeout);
});
// Clin Db Connection
services.Configure(opts =>
{
- opts.ConnectionString = config.GetByProxy(Config.Db.Clin.Connection);
+ opts.ConnectionString = "Server=127.0.0.1,1432;Database=SynPuf_OMOP;uid=sa;Password=Jefferson407!;"; //config.GetByProxy(Config.Db.Clin.Connection);
opts.DefaultTimeout = config.GetValue(Config.Db.Clin.DefaultTimeout);
opts.WithRdbms(config.GetValue(Config.Db.Clin.RDBMS));
opts.Cohort.WithQueryStrategy(config.GetValue(Config.Db.Clin.Cohort.QueryStrategy));
diff --git a/src/server/API/Options/StartupExtensions.Services.cs b/src/server/API/Options/StartupExtensions.Services.cs
index 7a8efc597..ab117fff3 100644
--- a/src/server/API/Options/StartupExtensions.Services.cs
+++ b/src/server/API/Options/StartupExtensions.Services.cs
@@ -9,6 +9,8 @@
using API.Jwt;
using API.Middleware.Federation;
using API.Middleware.Logging;
+using API.Integration.Shrine;
+using API.Integration.Shrine4_1;
using Microsoft.AspNetCore.Hosting;
using Microsoft.Extensions.DependencyInjection;
using Microsoft.Extensions.Hosting;
@@ -25,6 +27,7 @@
using Model.Compiler.SqlBuilder;
using Model.Compiler.PanelSqlCompiler;
using Model.Export;
+using Model.Integration.Shrine;
using Model.Network;
using Model.Options;
using Model.Search;
@@ -47,6 +50,7 @@
using Services.Import;
using Services.Notification;
using Services.Obfuscation;
+using System.Net.Http;
namespace API.Options
{
@@ -59,6 +63,7 @@ public static IServiceCollection RegisterLeafServices(
services.AddHttpContextAccessor();
services.AddScoped();
+ services.AddScoped();
services.AddTransient();
services.AddTransient();
@@ -91,6 +96,11 @@ public static IServiceCollection RegisterLeafServices(
client.DefaultRequestHeaders.Add("Accept", @"application/json");
});
+ services.AddHttpClient(client =>
+ {
+ client.DefaultRequestHeaders.Add("Accept", @"application/json");
+ });
+
if (environment.IsProduction())
{
services.AddHostedService();
@@ -121,6 +131,7 @@ public static IServiceCollection RegisterLeafServices(
services.AddTransient();
services.AddTransient();
+ services.AddIntegrationServices(environment);
services.AddAdminServices();
services.RegisterLeafCore();
@@ -182,6 +193,42 @@ static IServiceCollection AddIAMServices(this IServiceCollection services)
return services;
}
+ static IServiceCollection AddIntegrationServices(this IServiceCollection services, Microsoft.AspNetCore.Hosting.IHostingEnvironment environment)
+ {
+ var sp = services.BuildServiceProvider();
+ var integrationOpts = sp.GetRequiredService>().Value;
+
+ if (integrationOpts.Enabled)
+ {
+ if (integrationOpts.SHRINE.Enabled)
+ {
+ services.AddHostedService();
+ services.AddHostedService();
+ services.AddTransient();
+ services.AddTransient();
+ services.AddTransient();
+ services.AddSingleton();
+ services.AddSingleton();
+
+ /* Use for testing only!! */
+ if (!environment.IsProduction())
+ {
+ services.AddHttpClient().ConfigurePrimaryHttpMessageHandler(() => new HttpClientHandler
+ {
+ ClientCertificateOptions = ClientCertificateOption.Manual,
+ //ServerCertificateCustomValidationCallback = HttpClientHandler.DangerousAcceptAnyServerCertificateValidator,
+ ServerCertificateCustomValidationCallback = (request, cert, chain, errors) =>
+ {
+ return true;
+ }
+ });
+ }
+ }
+ }
+
+ return services;
+ }
+
static IServiceCollection AddCohortQueryExecutionService(this IServiceCollection services)
{
var sp = services.BuildServiceProvider();
diff --git a/src/server/API/appsettings.json b/src/server/API/appsettings.json
index 7200af4ef..07071a191 100644
--- a/src/server/API/appsettings.json
+++ b/src/server/API/appsettings.json
@@ -18,7 +18,7 @@
"DefaultTimeout": 180,
"RDBMS": "MSSQL",
"Cohort": {
- "QueryStrategy": "PARALLEL",
+ "QueryStrategy": "CTE",
"MaxParallelThreads": 5
}
}
@@ -62,8 +62,10 @@
},
"Compiler": {
"Alias": "@",
- "FieldPersonId": "person_id",
- "FieldEncounterId": "visit_occurrence_id"
+ //"FieldPersonId": "person_id",
+ //"FieldEncounterId": "visit_occurrence_id",
+ "FieldPersonId": "PatientDurableKey",
+ "FieldEncounterId": "EncounterDurableKey"
},
"Cohort": {
"RowLimit": 200000,
@@ -83,6 +85,28 @@
"Enabled": true
}
},
+ "Integration": {
+ "Enabled": true,
+ "SHRINE": {
+ "Enabled": true,
+ "HubApiURI": "https://localhost:6443",
+ "Node": {
+ "Id": 8304711555476111654,
+ "Key": "leaftest",
+ "Name": "leaftest"
+ },
+ "Researcher": {
+ "Id": 24823904,
+ "Name": "demo",
+ "Domain": "i2b2demo"
+ },
+ "Topic": {
+ "Id": 1481654093,
+ "Name": "Testing",
+ "Description": "This is a topic for testing SHRINE 2020 (1)"
+ }
+ }
+ },
"Import": {
"REDCap": {
"Enabled": false,
@@ -102,13 +126,13 @@
"Cohort": {
"Enabled": true,
"Noise": {
- "Enabled": false,
- "LowerBound": -10,
- "UpperBound": 10
+ "Enabled": true,
+ "LowerBound": -3,
+ "UpperBound": 3
},
"LowCellSizeMasking": {
- "Enabled": false,
- "Threshold": 10
+ "Enabled": true,
+ "Threshold": 3
}
}
},
diff --git a/src/server/Model/Authorization/UserContextProvider.cs b/src/server/Model/Authorization/UserContextProvider.cs
new file mode 100644
index 000000000..7a895ad8f
--- /dev/null
+++ b/src/server/Model/Authorization/UserContextProvider.cs
@@ -0,0 +1,41 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using Model.Error;
+
+namespace Model.Authorization
+{
+ public interface IUserContextProvider
+ {
+ void SetUserContext(IUserContext userContext);
+ IUserContext GetUserContext();
+ }
+
+ public class UserContextProvider : IUserContextProvider
+ {
+ IUserContext userContext;
+
+ public UserContextProvider(IUserContext userContext = null)
+ {
+ if (userContext != null)
+ {
+ this.userContext = userContext;
+ }
+ }
+
+ public void SetUserContext(IUserContext userContext)
+ {
+ this.userContext = userContext;
+ }
+
+ public IUserContext GetUserContext()
+ {
+ if (userContext == null) throw new LeafAuthorizationException("No user context is available");
+ return userContext;
+ }
+ }
+}
+
diff --git a/src/server/Model/Cohort/CohortCounter.cs b/src/server/Model/Cohort/CohortCounter.cs
index 9a9edf73a..e2dcf06a7 100644
--- a/src/server/Model/Cohort/CohortCounter.cs
+++ b/src/server/Model/Cohort/CohortCounter.cs
@@ -54,8 +54,8 @@ public CohortCounter(
IPatientCohortService counter,
ICohortCacheService cohortCache,
IObfuscationService obfuscator,
- IUserContext user,
- ILogger log)
+ ILogger log,
+ IUserContextProvider userContextProvider)
{
this.runtime = opts.Value.Runtime;
this.deidentOpts = deidentOpts.Value;
@@ -64,7 +64,7 @@ public CohortCounter(
this.counter = counter;
this.obfuscator = obfuscator;
this.cohortCache = cohortCache;
- this.user = user;
+ this.user = userContextProvider.GetUserContext();
this.log = log;
}
@@ -180,6 +180,16 @@ async Task FullCount(IPatientCountQueryDTO queryDTO, CancellationToken t
token.ThrowIfCancellationRequested();
+ // DEBUGGING ONLY
+ return new Result
+ {
+ ValidationContext = ctx,
+ Count = new PatientCount
+ {
+ SqlStatements = cohort.SqlStatements
+ }
+ };
+
var cached = await CacheCohort(cohort);
var result = new Result
{
diff --git a/src/server/Model/Cohort/DemographicProvider.cs b/src/server/Model/Cohort/DemographicProvider.cs
index 4fffeb9c7..838cf33cd 100644
--- a/src/server/Model/Cohort/DemographicProvider.cs
+++ b/src/server/Model/Cohort/DemographicProvider.cs
@@ -39,23 +39,26 @@ Task ExecuteDemographicsAsync(
readonly IUserContext user;
readonly ClientOptions clientOpts;
readonly DeidentificationOptions deidentOpts;
+ readonly IntegrationOptions integrationOpts;
readonly ILogger log;
- public DemographicProvider (
- IUserContext user,
+ public DemographicProvider(
+ IUserContextProvider userContextProvider,
DemographicCompilerValidationContextProvider contextProvider,
IOptions clientOpts,
IOptions deidentOpts,
+ IOptions integrationOpts,
IDemographicSqlCompiler compiler,
IDemographicsExecutor executor,
ILogger log)
{
- this.user = user;
+ this.user = userContextProvider.GetUserContext();
this.contextProvider = contextProvider;
this.compiler = compiler;
this.executor = executor;
this.clientOpts = clientOpts.Value;
this.deidentOpts = deidentOpts.Value;
+ this.integrationOpts = integrationOpts.Value;
this.log = log;
}
@@ -130,7 +133,7 @@ void ThrowIfSettingsInvalid()
{
throw new Exception("Both Visualize and Patient List are disabled");
}
- if (deidentOpts.Cohort.Noise.Enabled)
+ if (deidentOpts.Cohort.Noise.Enabled && !integrationOpts.Enabled)
{
throw new Exception("Demographics cannot be returned if Cohort De-identification Noise is enabled");
}
diff --git a/src/server/Model/Compiler/NumericFilterType.cs b/src/server/Model/Compiler/NumericFilterType.cs
index fd5a4a58b..76a943bb1 100644
--- a/src/server/Model/Compiler/NumericFilterType.cs
+++ b/src/server/Model/Compiler/NumericFilterType.cs
@@ -10,10 +10,10 @@ public enum NumericFilterType
{
None,
GreaterThan,
- GreaterThanOrEqualTo,
+ GreaterThanOrEqual,
LessThan,
- LessThanOrEqualTo,
- EqualTo,
+ LessThanOrEqual,
+ Equal,
Between
}
}
diff --git a/src/server/Model/Compiler/PanelConverter.cs b/src/server/Model/Compiler/PanelConverter.cs
index 97e77ed02..ad96ef2db 100644
--- a/src/server/Model/Compiler/PanelConverter.cs
+++ b/src/server/Model/Compiler/PanelConverter.cs
@@ -33,12 +33,12 @@ public class PanelConverter
public PanelConverter(
PreflightResourceChecker preflightSearch,
- IUserContext userContext,
+ IUserContextProvider userContextProvider,
IOptions compilerOptions,
ICachedCohortPreparer cohortPreparer,
ILogger logger)
{
- user = userContext;
+ this.user = userContextProvider.GetUserContext();
this.preflightSearch = preflightSearch;
this.compilerOptions = compilerOptions.Value;
this.cohortPreparer = cohortPreparer;
@@ -120,7 +120,7 @@ public async Task GetPanelsAsync(IQueryDefinition query)
/// The panels.
/// PanelDTOs.
/// Import panel items referenced in panels.
- public IEnumerable CrosswalkImportIds(IEnumerable panels, IEnumerable importRefs)
+ public static IEnumerable CrosswalkImportIds(IEnumerable panels, IEnumerable importRefs)
{
var mapped = panels.Select(p => p).ToList();
@@ -152,7 +152,12 @@ public void LocalizeDefinition(IQueryDefinition definition, PatientCountQuery lo
var map = new Dictionary(localQuery.Panels
.GetConcepts()
- .Select(c => new KeyValuePair(key: c.UniversalId.ToString(), value: new ResourceRef { Id = c.Id, UniversalId = c.UniversalId.ToString() })));
+ .Select(c =>
+ new KeyValuePair(
+ key: c.UniversalId.ToString(),
+ value: new ResourceRef { Id = c.Id, UniversalId = c.UniversalId.ToString() })
+ )
+ );
var items = definition.Panels
.SelectMany(p => p.SubPanels)
@@ -217,7 +222,7 @@ IEnumerable GetPanels(IEnumerable panels, IEnumerable
return GetPanels(panels, feder);
}
- IEnumerable GetPanels(IEnumerable panels, LocalConceptMap concepts)
+ static IEnumerable GetPanels(IEnumerable panels, LocalConceptMap concepts)
{
var converted = new List();
@@ -230,7 +235,7 @@ IEnumerable GetPanels(IEnumerable panels, LocalConceptMap conc
return converted;
}
- ICollection GetSubPanels(IEnumerable dtos, LocalConceptMap concepts)
+ static ICollection GetSubPanels(IEnumerable dtos, LocalConceptMap concepts)
{
var subs = new List();
@@ -244,7 +249,7 @@ ICollection GetSubPanels(IEnumerable dtos, LocalConceptM
return subs;
}
- IEnumerable GetPanelItems(IEnumerable dtos, LocalConceptMap concepts)
+ static IEnumerable GetPanelItems(IEnumerable dtos, LocalConceptMap concepts)
{
var items = new List();
@@ -257,7 +262,7 @@ IEnumerable GetPanelItems(IEnumerable dtos, LocalConce
return items;
}
- IEnumerable GetPanels(IEnumerable panels, FederatedConceptMap concepts)
+ static IEnumerable GetPanels(IEnumerable panels, FederatedConceptMap concepts)
{
var converted = new List();
@@ -270,7 +275,7 @@ IEnumerable GetPanels(IEnumerable panels, FederatedConceptMap
return converted;
}
- ICollection GetSubPanels(IEnumerable dtos, FederatedConceptMap concepts)
+ static ICollection GetSubPanels(IEnumerable dtos, FederatedConceptMap concepts)
{
var subs = new List();
@@ -284,7 +289,7 @@ ICollection GetSubPanels(IEnumerable dtos, FederatedConc
return subs;
}
- IEnumerable GetPanelItems(IEnumerable dtos, FederatedConceptMap concepts)
+ static IEnumerable GetPanelItems(IEnumerable dtos, FederatedConceptMap concepts)
{
var items = new List();
diff --git a/src/server/Model/Compiler/PanelItem.cs b/src/server/Model/Compiler/PanelItem.cs
index 3832a9b2d..9d4b59921 100644
--- a/src/server/Model/Compiler/PanelItem.cs
+++ b/src/server/Model/Compiler/PanelItem.cs
@@ -13,7 +13,6 @@ public class PanelItem : BasePanelItem
{
public Concept Concept { get; set; }
public IEnumerable Specializations { get; set; }
- public string SqlRecencyFilter { get; set; }
public bool UseNumericFilter
{
get
diff --git a/src/server/Model/Compiler/PanelValidator.cs b/src/server/Model/Compiler/PanelValidator.cs
index ebaf27a50..23406d75b 100644
--- a/src/server/Model/Compiler/PanelValidator.cs
+++ b/src/server/Model/Compiler/PanelValidator.cs
@@ -213,11 +213,11 @@ void throwIfNotLength(int expected)
switch (filter.FilterType)
{
- case NumericFilterType.EqualTo:
+ case NumericFilterType.Equal:
case NumericFilterType.GreaterThan:
- case NumericFilterType.GreaterThanOrEqualTo:
+ case NumericFilterType.GreaterThanOrEqual:
case NumericFilterType.LessThan:
- case NumericFilterType.LessThanOrEqualTo:
+ case NumericFilterType.LessThanOrEqual:
throwIfNotLength(1);
return;
case NumericFilterType.Between:
diff --git a/src/server/Model/Compiler/SqlBuilder/PanelItemSqlSet.cs b/src/server/Model/Compiler/SqlBuilder/PanelItemSqlSet.cs
index a25c5f9bf..796176978 100644
--- a/src/server/Model/Compiler/SqlBuilder/PanelItemSqlSet.cs
+++ b/src/server/Model/Compiler/SqlBuilder/PanelItemSqlSet.cs
@@ -24,12 +24,31 @@ public PanelItemSequentialSqlSet(
internal override void SetSelect()
{
- Select = new[] { PersonId, EncounterId, Date, EventId };
+ if (!panelitem.UseRecencyFilter)
+ {
+ Select = new[] { PersonId, EncounterId, Date, EventId };
+ }
+ else
+ {
+ Select = new ISelectable[] { PersonId, EncounterId, AggregateDate, EventId };
+ }
}
internal override void SetGroupBy()
{
- // Do nothing. Group By clauses in a sequence are added in the parent PanelSequentialSqlSet.
+ if (panelitem.UseRecencyFilter)
+ {
+ if (concept.IsEventBased)
+ {
+ GroupBy = new[] { PersonId, EncounterId, EventId };
+ }
+ else
+ {
+ GroupBy = new[] { PersonId, EncounterId };
+ }
+ }
+
+ // Otherwise do nothing. Group By clauses in a sequence are added in the parent PanelSequentialSqlSet.
}
internal override void SetHaving()
@@ -41,17 +60,18 @@ internal override void SetHaving()
class PanelItemSqlSet : NamedSet
{
- readonly CompilerOptions compilerOptions;
- readonly Panel panel;
- readonly SubPanel subpanel;
- readonly PanelItem panelitem;
- readonly Concept concept;
+ readonly internal CompilerOptions compilerOptions;
+ readonly internal Panel panel;
+ readonly internal SubPanel subpanel;
+ readonly internal PanelItem panelitem;
+ readonly internal Concept concept;
readonly List where = new List();
internal ISqlDialect dialect;
internal Column PersonId;
internal Column EncounterId;
internal EventIdColumn EventId;
+ internal ExpressedColumn AggregateDate;
internal AutoAliasedColumn Date;
internal AutoAliasedColumn Number;
@@ -101,6 +121,12 @@ void SetColumns()
{
EncounterId = new Column(compilerOptions.FieldEncounterId, this);
Date = new AutoAliasedColumn(concept.SqlFieldDate, aliasMarker, this);
+
+ if (panelitem.UseRecencyFilter)
+ {
+ var op = panelitem.RecencyFilter == RecencyFilterType.Min ? "MIN" : "MAX";
+ AggregateDate = new ExpressedColumn(new Expression($"{op}({Date})"), Date.Name.Replace(aliasMarker + ".", ""));
+ }
}
if (concept.IsEventBased)
{
@@ -163,7 +189,7 @@ void CheckDate()
var start = GetDateExpression(panel.DateFilter.Start);
var end = GetDateExpression(panel.DateFilter.End, true);
- if (panel.PanelType == PanelType.Sequence && subpanel.Index > 0)
+ if (panel.PanelType == PanelType.Sequence && subpanel.Index > 0 && !panelitem.UseRecencyFilter)
{
var offset = new Expression(dialect.DateAdd(DateIncrementType.Month, -6, start));
where.Add(Date >= offset);
@@ -198,16 +224,16 @@ void CheckNumericFilter()
case NumericFilterType.GreaterThan:
where.Add(Number > val1);
return;
- case NumericFilterType.GreaterThanOrEqualTo:
+ case NumericFilterType.GreaterThanOrEqual:
where.Add(Number >= val1);
return;
case NumericFilterType.LessThan:
where.Add(Number < val1);
return;
- case NumericFilterType.LessThanOrEqualTo:
+ case NumericFilterType.LessThanOrEqual:
where.Add(Number <= val1);
return;
- case NumericFilterType.EqualTo:
+ case NumericFilterType.Equal:
where.Add(Number == val1);
return;
case NumericFilterType.Between:
diff --git a/src/server/Model/Compiler/SqlBuilder/PanelSqlCompiler.cs b/src/server/Model/Compiler/SqlBuilder/PanelSqlCompiler.cs
index 7abf52b60..fe7c1738a 100644
--- a/src/server/Model/Compiler/SqlBuilder/PanelSqlCompiler.cs
+++ b/src/server/Model/Compiler/SqlBuilder/PanelSqlCompiler.cs
@@ -22,11 +22,11 @@ public class PanelSqlCompiler : IPanelSqlCompiler
readonly CompilerOptions compilerOptions;
public PanelSqlCompiler(
- IUserContext user,
+ IUserContextProvider userContextProvider,
ISqlDialect dialect,
IOptions compilerOptions)
{
- this.user = user;
+ this.user = userContextProvider.GetUserContext();
this.dialect = dialect;
this.compilerOptions = compilerOptions.Value;
}
@@ -51,7 +51,7 @@ public string BuildPanelSql(Panel panel)
default:
return string.Empty;
}
- ValidateSql(sql);
+ //ValidateSql(sql);
return sql;
}
diff --git a/src/server/Model/Compiler/SqlBuilder/SubPanelSqlSet.cs b/src/server/Model/Compiler/SqlBuilder/SubPanelSqlSet.cs
index f12fead86..3d79a13c2 100644
--- a/src/server/Model/Compiler/SqlBuilder/SubPanelSqlSet.cs
+++ b/src/server/Model/Compiler/SqlBuilder/SubPanelSqlSet.cs
@@ -57,8 +57,8 @@ void SetSelect()
PersonId = new Column(first.PersonId);
EncounterId = new Column(first.EncounterId);
- Date = new AutoAliasedColumn(first.Date.Name, first.Date.AliasMarker);
EventId = new EventIdColumn(first.EventId);
+ Date = new AutoAliasedColumn(first.Date.Name, first.Date.AliasMarker);
}
}
}
diff --git a/src/server/Model/Compiler/SubPanel.cs b/src/server/Model/Compiler/SubPanel.cs
index c7d8a55fc..083e88dad 100644
--- a/src/server/Model/Compiler/SubPanel.cs
+++ b/src/server/Model/Compiler/SubPanel.cs
@@ -5,7 +5,6 @@
// file, You can obtain one at http://mozilla.org/MPL/2.0/.
using System;
using System.Collections.Generic;
-using System.Linq;
namespace Model.Compiler
{
diff --git a/src/server/Model/Error/LeafAuthorizationException.cs b/src/server/Model/Error/LeafAuthorizationException.cs
new file mode 100644
index 000000000..55b2276a4
--- /dev/null
+++ b/src/server/Model/Error/LeafAuthorizationException.cs
@@ -0,0 +1,26 @@
+// Copyright (c) 2021, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+
+namespace Model.Error
+{
+ public class LeafAuthorizationException : ApplicationException
+ {
+ public LeafErrorCode ErrorCode { get; private set; } = LeafErrorCode.Forbidden;
+
+ public LeafAuthorizationException()
+ {
+ }
+
+ public LeafAuthorizationException(string message) : base(message)
+ {
+ }
+
+ public LeafAuthorizationException(string message, Exception innerException) : base(message, innerException)
+ {
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/server/Model/Integration/Shrine/4_1/ShrineExpression.cs b/src/server/Model/Integration/Shrine/4_1/ShrineExpression.cs
new file mode 100644
index 000000000..2004ec5ed
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/4_1/ShrineExpression.cs
@@ -0,0 +1,119 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using System.Collections.Generic;
+using Model.Compiler;
+
+namespace Model.Integration.Shrine4_1
+{
+ public class ShrineQueryDefinition
+ {
+ public ShrineConjunction Expression { get; set; }
+ }
+
+ public abstract class ShrineExpression
+ {
+ public int NMustBeTrue { get; set; }
+ public DateTime? StartDate { get; set; }
+ public DateTime? EndDate { get; set; }
+ public int? OccursAtLeast { get; set; }
+ public ShrineConjunction Concepts { get; set; }
+ public ShrineConjunctionCompare Compare { get; set; } = new ShrineConjunctionCompare();
+ }
+
+ public abstract class ShrineGroup : ShrineExpression
+ {
+
+ }
+
+ public class ShrineConjunction : ShrineExpression
+ {
+ public IEnumerable Possibilities { get; set; } = new List();
+ }
+
+ public class ShrineConceptGroupOrTimeline : ShrineConceptGroup
+ {
+ public ShrineConceptGroup First { get; set; }
+ public IEnumerable Subsequent { get; set; } = new List();
+
+ public bool IsConceptGroup => First == null;
+ public bool IsTimeline => First != null;
+ }
+
+ public class ShrineTimelineSubsequentEvent
+ {
+ public ShrineConceptGroup ConceptGroup { get; set; }
+ public ShrineOccurrence PreviousOccurrence { get; set; }
+ public ShrineOccurrence ThisOccurrence { get; set; }
+ public ShrineTimelineSubsequentEventTimeConstraint TimeConstraint { get; set; }
+
+ public ShrineTimelineSubsequentEvent() { }
+ }
+
+ public class ShrineTimelineSubsequentEventTimeConstraint
+ {
+ public NumericFilterType Operator { get; set; }
+ public DateIncrementType TimeUnit { get; set; }
+ public int Value { get; set; }
+ }
+
+ public class ShrineConceptConjunction : ShrineExpression
+ {
+ public IEnumerable Possibilities { get; set; } = new List();
+ }
+
+ public class ShrineConceptGroup : ShrineGroup
+ {
+ public new ShrineConceptConjunction Concepts { get; set; }
+ }
+
+ public class ShrineTimelineGroup : ShrineGroup
+ {
+ public ShrineConceptGroup ConceptGroup { get; set; }
+
+ }
+
+ public class ShrineTimeline : ShrineGroup
+ {
+ public ShrineConceptGroup First { get; set; }
+ public IEnumerable Subsequent { get; set; }
+ }
+
+ public class ShrineConcept : ShrineExpression
+ {
+ public string DisplayName { get; set; }
+ public string TermPath { get; set; }
+ public ShrineConceptConstraint Constraint { get; set; }
+ }
+
+ public class ShrineConceptConstraint
+ {
+ public NumericFilterType Operator { get; set; }
+ public decimal? Value { get; set; }
+ public decimal? Value1 { get; set; }
+ public decimal? Value2 { get; set; }
+ public string Unit { get; set; }
+ }
+
+ public class ShrineConjunctionCompare
+ {
+ public ShrineConjunctionComparison EncodedClass { get; set; } = ShrineConjunctionComparison.AtLeast;
+ }
+
+ public enum ShrineConjunctionComparison
+ {
+ AtLeast,
+ Exactly,
+ AtMost
+ }
+
+ public enum ShrineOccurrence
+ {
+ Any,
+ First
+ }
+}
+
diff --git a/src/server/Model/Integration/Shrine/4_1/ShrineQuery.cs b/src/server/Model/Integration/Shrine/4_1/ShrineQuery.cs
new file mode 100644
index 000000000..c3555588b
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/4_1/ShrineQuery.cs
@@ -0,0 +1,45 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using Model.Integration.Shrine;
+
+namespace Model.Integration.Shrine4_1
+{
+ public class ShrineQuery
+ {
+ public long Id { get; set; }
+ public ShrineVersionInfo VersionInfo { get; set; }
+ public ShrineQueryDefinition QueryDefinition { get; set; }
+ public ShrineStatusType Status { get; set; }
+ public ShrineOutputType Output { get; set; }
+ public string QueryName { get; set; }
+ public long NodeOfOriginId { get; set; }
+ public long ResearcherId { get; set; }
+ public long TopicId { get; set; }
+ public string ProjectName { get; set; }
+ public bool Flagged { get; set; } = false;
+ public string FlaggedMessage { get; set; }
+ public ShrineQueryType EncodedClass { get; set; }
+ }
+
+ public enum ShrineQueryType
+ {
+ QueryProgress
+ }
+
+ public enum ShrineOutputType
+ {
+ Count,
+ DemographicsAndCount
+ }
+
+ public enum ShrineStatusType
+ {
+ ReadyForAdapters,
+ SentToHub
+ }
+}
+
diff --git a/src/server/Model/Integration/Shrine/IShrineQueryResultCache.cs b/src/server/Model/Integration/Shrine/IShrineQueryResultCache.cs
new file mode 100644
index 000000000..7b6abdbc5
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/IShrineQueryResultCache.cs
@@ -0,0 +1,140 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Threading;
+using System.Collections;
+
+namespace Model.Integration.Shrine
+{
+ public interface IShrineQueryResultCache : IEnumerable
+ {
+ IEnumerable All();
+ ShrineQueryResult GetOrDefault(long id);
+ ShrineQueryResult PopOrDefault(long id);
+ void Put(ShrineQueryResult result);
+ void Put(ShrineResultProgress nodeResult);
+ void Put(long id, ShrineResearcher user);
+ void Put(IEnumerable nodeResults);
+ int DeleteOlderThan(DateTime earliest);
+ }
+
+ public class ShrineQueryResultCache : IShrineQueryResultCache
+ {
+ readonly Dictionary store = new();
+ readonly ReaderWriterLockSlim sync = new();
+
+ public ShrineQueryResultCache(IEnumerable initial)
+ {
+
+ store = initial.ToDictionary(ne => ne.Id);
+ sync = new ReaderWriterLockSlim();
+ }
+
+ public IEnumerable All()
+ {
+ sync.EnterReadLock();
+ var all = store.Values;
+ sync.ExitReadLock();
+ return all;
+ }
+
+ public ShrineQueryResult GetOrDefault(long id)
+ {
+ sync.EnterReadLock();
+ store.TryGetValue(id, out var result);
+ sync.ExitReadLock();
+ return result;
+ }
+
+ public void Put(ShrineQueryResult result)
+ {
+ sync.EnterWriteLock();
+ store[result.Id] = result;
+ store[result.Id].Updated = DateTime.Now;
+ sync.ExitWriteLock();
+ }
+
+ public void Put(long id, ShrineResearcher user)
+ {
+ sync.EnterWriteLock();
+ if (!store.ContainsKey(id))
+ {
+ store[id] = new ShrineQueryResult(id);
+ }
+ store[id].User = user;
+ sync.ExitWriteLock();
+ }
+
+ public void Put(ShrineResultProgress nodeResult)
+ {
+ sync.EnterWriteLock();
+ if (!store.ContainsKey(nodeResult.QueryId))
+ {
+ store[nodeResult.QueryId] = new ShrineQueryResult(nodeResult.QueryId);
+ }
+ store[nodeResult.QueryId].Results[nodeResult.AdapterNodeId] = nodeResult;
+ store[nodeResult.QueryId].Updated = DateTime.Now;
+ sync.ExitWriteLock();
+ }
+
+ public void Put(IEnumerable nodeResults)
+ {
+ if (!nodeResults.Any()) return;
+
+ sync.EnterWriteLock();
+ var first = nodeResults.First();
+ if (!store.ContainsKey(first.QueryId))
+ {
+ store[first.QueryId] = new ShrineQueryResult(first.QueryId);
+ }
+ foreach (var nodeResult in nodeResults)
+ {
+ store[first.QueryId].Results[nodeResult.AdapterNodeId] = nodeResult;
+ }
+ store[first.QueryId].Updated = DateTime.Now;
+ sync.ExitWriteLock();
+ }
+
+ public ShrineQueryResult PopOrDefault(long id)
+ {
+ sync.EnterWriteLock();
+ store.Remove(id, out var result);
+ sync.ExitWriteLock();
+ return result;
+ }
+
+ public int DeleteOlderThan(DateTime earliest)
+ {
+ var deleteCount = 0;
+
+ sync.EnterWriteLock();
+ foreach (var result in All())
+ {
+ if (result.Updated < earliest)
+ {
+ store.Remove(result.Id, out var _);
+ deleteCount++;
+ }
+ }
+ sync.ExitWriteLock();
+
+ return deleteCount;
+ }
+
+ public IEnumerator GetEnumerator()
+ {
+ return All().GetEnumerator();
+ }
+
+ IEnumerator IEnumerable.GetEnumerator()
+ {
+ return GetEnumerator();
+ }
+ }
+}
+
diff --git a/src/server/Model/Integration/Shrine/IShrineUserQueryCache.cs b/src/server/Model/Integration/Shrine/IShrineUserQueryCache.cs
new file mode 100644
index 000000000..5260bc1e6
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/IShrineUserQueryCache.cs
@@ -0,0 +1,105 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using System.Collections;
+using System.Collections.Generic;
+using System.Threading;
+using Model.Authorization;
+using Model.Compiler;
+
+namespace Model.Integration.Shrine
+{
+ public interface IShrineUserQueryCache : IEnumerable
+ {
+ IEnumerable All();
+ ShrineUserQueryEntry GetOrDefault(long id);
+ ShrineUserQueryEntry PopOrDefault(long id);
+ void Put(long id, IUserContext user, IPatientCountQueryDTO query);
+ int DeleteOlderThan(DateTime earliest);
+ }
+
+ public class ShrineUserContextCache : IShrineUserQueryCache
+ {
+ readonly Dictionary store = new();
+ readonly ReaderWriterLockSlim sync = new();
+
+ public IEnumerable All()
+ {
+ sync.EnterReadLock();
+ var all = store.Values;
+ sync.ExitReadLock();
+ return all;
+ }
+
+ public ShrineUserQueryEntry GetOrDefault(long id)
+ {
+ sync.EnterReadLock();
+ store.TryGetValue(id, out var result);
+ sync.ExitReadLock();
+ return result;
+ }
+
+ public ShrineUserQueryEntry PopOrDefault(long id)
+ {
+ sync.EnterWriteLock();
+ store.Remove(id, out var result);
+ sync.ExitWriteLock();
+ return result;
+ }
+
+ public void Put(long id, IUserContext user, IPatientCountQueryDTO query)
+ {
+ sync.EnterWriteLock();
+ store[id] = new ShrineUserQueryEntry(user, query, id);
+ sync.ExitWriteLock();
+ }
+
+ public int DeleteOlderThan(DateTime earliest)
+ {
+ var deleteCount = 0;
+
+ sync.EnterWriteLock();
+ foreach (var user in All())
+ {
+ if (user.Added < earliest)
+ {
+ store.Remove(user.QueryId, out var _);
+ deleteCount++;
+ }
+ }
+ sync.ExitWriteLock();
+
+ return deleteCount;
+ }
+
+ public IEnumerator GetEnumerator()
+ {
+ return All().GetEnumerator();
+ }
+
+ IEnumerator IEnumerable.GetEnumerator()
+ {
+ return GetEnumerator();
+ }
+ }
+
+ public class ShrineUserQueryEntry
+ {
+ public IUserContext User { get; }
+ public IPatientCountQueryDTO Query { get; }
+ public long QueryId { get; }
+ public DateTime Added { get; set; }
+
+ public ShrineUserQueryEntry(IUserContext user, IPatientCountQueryDTO query, long queryId)
+ {
+ User = user;
+ Query = query;
+ QueryId = queryId;
+ Added = DateTime.Now;
+ }
+ }
+}
+
diff --git a/src/server/Model/Integration/Shrine/ShrineCohortCounter.cs b/src/server/Model/Integration/Shrine/ShrineCohortCounter.cs
new file mode 100644
index 000000000..11649d516
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/ShrineCohortCounter.cs
@@ -0,0 +1,64 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using Microsoft.Extensions.Logging;
+using Microsoft.Extensions.Options;
+using Model.Authorization;
+using Model.Options;
+using Model.Integration.Shrine4_1;
+using Model.Compiler;
+
+namespace Model.Integration.Shrine
+{
+ public class ShrineCohortCounter
+ {
+ readonly ILogger log;
+ readonly IUserContext user;
+ readonly IShrineUserQueryCache userQueryCache;
+ readonly IShrineQueryResultCache queryResultCache;
+ readonly ShrineIntegrationOptions opts;
+
+ public ShrineCohortCounter(
+ ILogger log,
+ IOptions opts,
+ IUserContext user,
+ IShrineUserQueryCache userQueryCache,
+ IShrineQueryResultCache queryResultCache)
+ {
+ this.user = user;
+ this.userQueryCache = userQueryCache;
+ this.queryResultCache = queryResultCache;
+ this.log = log;
+ this.opts = opts.Value;
+ }
+
+ public ShrineRunQueryForResult SubmitQueryToShrine(ShrineQuery query)
+ {
+ return new ShrineRunQueryForResult
+ {
+ Query = query,
+ Researcher = new ShrineResearcher
+ {
+ Id = opts.Researcher.Id,
+ VersionInfo = query.VersionInfo,
+ UserName = opts.Researcher.Name,
+ UserDomainName = opts.Researcher.Domain,
+ NodeId = opts.Node.Id
+ },
+ Topic = new ShrineTopic
+ {
+ Id = opts.Topic.Id,
+ VersionInfo = query.VersionInfo,
+ ResearcherId = opts.Researcher.Id,
+ Name = opts.Topic.Name,
+ Description = opts.Topic.Description
+ },
+ ProtocolVersion = 2
+ };
+ }
+ }
+}
+
diff --git a/src/server/Model/Integration/Shrine/ShrineDeliveryAttempt.cs b/src/server/Model/Integration/Shrine/ShrineDeliveryAttempt.cs
new file mode 100644
index 000000000..cd16c0e46
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/ShrineDeliveryAttempt.cs
@@ -0,0 +1,41 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+
+namespace Model.Integration.Shrine
+{
+ public class ShrineDeliveryAttempt
+ {
+ public ShrineInnerDeliveryAttempt DeliveryAttemptId { get; set; } = new ShrineInnerDeliveryAttempt();
+ public long MillisecondsToComplete { get; set; }
+ public int RemainingAttempts { get; set; }
+ public string Contents { get; set; }
+ }
+
+ public class ShrineInnerDeliveryAttempt
+ {
+ public long Underlying { get; set; }
+ }
+
+ public class ShrineDeliveryContents
+ {
+ public string Contents { get; set; }
+ public long ContentsSubject { get; set; }
+ public ShrineDeliveryContentsType ContentsType { get; set; }
+ public int ProtocolVersion = 2;
+ }
+
+ public enum ShrineDeliveryContentsType
+ {
+ Unknown,
+ UpdateQueryAtQep,
+ RunQueryForResult,
+ RunQueryAtHub,
+ Result,
+ UpdateResult
+ }
+}
+
diff --git a/src/server/Model/Integration/Shrine/ShrineNode.cs b/src/server/Model/Integration/Shrine/ShrineNode.cs
new file mode 100644
index 000000000..2bff23afb
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/ShrineNode.cs
@@ -0,0 +1,23 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+namespace Model.Integration.Shrine
+{
+ public class ShrineNode
+ {
+ public long Id { get; set; }
+ public ShrineVersionInfo VersionInfo { get; set; }
+ public string Name { get; set; }
+ public string Key { get; set; }
+ public string UserDomainName { get; set; }
+ public string MomQueueName { get; set; }
+ public string AdminEmail { get; set; }
+ public bool SendQueries { get; set; }
+ public int UnderstandsProtocol { get; set; }
+ public string MomId { get; set; }
+ }
+}
+
diff --git a/src/server/Model/Integration/Shrine/ShrineQueryResult.cs b/src/server/Model/Integration/Shrine/ShrineQueryResult.cs
new file mode 100644
index 000000000..b34d79c3e
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/ShrineQueryResult.cs
@@ -0,0 +1,24 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using System.Collections.Generic;
+
+namespace Model.Integration.Shrine
+{
+ public class ShrineQueryResult
+ {
+ public long Id { get; set; }
+ public DateTime Updated = DateTime.Now;
+ public ShrineResearcher User { get; set; }
+ public Dictionary Results = new();
+
+ public ShrineQueryResult(long id)
+ {
+ Id = id;
+ }
+ }
+}
+
diff --git a/src/server/Model/Integration/Shrine/ShrineQueryStatus.cs b/src/server/Model/Integration/Shrine/ShrineQueryStatus.cs
new file mode 100644
index 000000000..cf2da07c2
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/ShrineQueryStatus.cs
@@ -0,0 +1,31 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+namespace Model.Integration.Shrine
+{
+ public class ShrineQueryStatus
+ {
+ public ShrineQueryStatusType EncodedClass { get; set; }
+ }
+
+ public enum ShrineQueryStatusType
+ {
+ Unknown,
+ SentToAdapters,
+ ReceivedAtHub,
+ UpdateQueryAtQepWithStatus,
+ UpdateQueryReadyForAdapters,
+ IdAssigned,
+ SubmittedToCRC,
+ ResultProgress,
+ ReceivedByAdapter,
+ CrcResult,
+ ResultFromCRC,
+ UpdateResultWithProgress,
+ UpdateResultWithCrcResult
+ }
+}
+
diff --git a/src/server/Model/Integration/Shrine/ShrineResearcher.cs b/src/server/Model/Integration/Shrine/ShrineResearcher.cs
new file mode 100644
index 000000000..03a4ec134
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/ShrineResearcher.cs
@@ -0,0 +1,18 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+namespace Model.Integration.Shrine
+{
+ public class ShrineResearcher
+ {
+ public long Id { get; set; }
+ public ShrineVersionInfo VersionInfo { get; set; }
+ public string UserName { get; set; }
+ public string UserDomainName { get; set; }
+ public long NodeId { get; set; }
+ }
+}
+
diff --git a/src/server/Model/Integration/Shrine/ShrineResultProgress.cs b/src/server/Model/Integration/Shrine/ShrineResultProgress.cs
new file mode 100644
index 000000000..1efa7d141
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/ShrineResultProgress.cs
@@ -0,0 +1,33 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+
+namespace Model.Integration.Shrine
+{
+ public class ShrineResultProgress
+ {
+ public long Id { get; set; }
+ public ShrineVersionInfo VersionInfo { get; set; }
+ public long QueryId { get; set; }
+ public long AdapterNodeId { get; set; }
+ public string AdapterNodeName { get; set; }
+ public ShrineQueryStatus Status { get; set; }
+ public string StatusMessage { get; set; }
+ public long? CrcQueryInstanceId { get; set; }
+ public ShrineQueryStatusType EncodedClass { get; set; }
+ public int Count { get; set; } = -1;
+ public ShrineResultObfuscatingParameters ObfuscatingParameters { get; set; }
+ }
+
+ public class ShrineResultObfuscatingParameters
+ {
+ public int BinSize { get; set; }
+ public decimal StdDev { get; set; }
+ public int NoiseClamp { get; set; }
+ public int LowLimit { get; set; }
+ }
+}
+
diff --git a/src/server/Model/Integration/Shrine/ShrineRunQueryForResult.cs b/src/server/Model/Integration/Shrine/ShrineRunQueryForResult.cs
new file mode 100644
index 000000000..4921c646f
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/ShrineRunQueryForResult.cs
@@ -0,0 +1,21 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using Model.Integration.Shrine4_1;
+
+namespace Model.Integration.Shrine
+{
+ public class ShrineRunQueryForResult
+ {
+ public ShrineQuery Query { get; set; }
+ public ShrineNode Node { get; set; }
+ public ShrineTopic Topic { get; set; }
+ public ShrineResultProgress ResultProgress { get; set; }
+ public ShrineResearcher Researcher { get; set; }
+ public int ProtocolVersion { get; set; }
+ }
+}
+
diff --git a/src/server/Model/Integration/Shrine/ShrineTopic.cs b/src/server/Model/Integration/Shrine/ShrineTopic.cs
new file mode 100644
index 000000000..9c79b182b
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/ShrineTopic.cs
@@ -0,0 +1,18 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+namespace Model.Integration.Shrine
+{
+ public class ShrineTopic
+ {
+ public long Id { get; set; }
+ public ShrineVersionInfo VersionInfo { get; set; }
+ public long ResearcherId { get; set; }
+ public string Name { get; set; }
+ public string Description { get; set; }
+ }
+}
+
diff --git a/src/server/Model/Integration/Shrine/ShrineUpdateQueryAtQep.cs b/src/server/Model/Integration/Shrine/ShrineUpdateQueryAtQep.cs
new file mode 100644
index 000000000..df219db96
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/ShrineUpdateQueryAtQep.cs
@@ -0,0 +1,30 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+using System.Linq;
+using System.Collections.Generic;
+
+namespace Model.Integration.Shrine
+{
+ public class ShrineUpdateQueryAtQep
+ {
+ public long QueryId { get; set; }
+ public ShrineQueryStatus QueryStatus { get; set; }
+ public DateTime ChangeDate { get; set; }
+ public ShrineQueryStatusType EncodedClass { get; set; }
+ public IEnumerable ResultProgresses { get; set; }
+
+ public ShrineQueryResult ToQueryResult()
+ {
+ return new ShrineQueryResult(QueryId)
+ {
+ Updated = ChangeDate,
+ Results = ResultProgresses?.ToDictionary(p => p.QueryId)
+ };
+ }
+ }
+}
+
diff --git a/src/server/Model/Integration/Shrine/ShrineUpdateResultWithCrcResult.cs b/src/server/Model/Integration/Shrine/ShrineUpdateResultWithCrcResult.cs
new file mode 100644
index 000000000..67b4bbdc8
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/ShrineUpdateResultWithCrcResult.cs
@@ -0,0 +1,21 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+namespace Model.Integration.Shrine
+{
+ public class ShrineUpdateResultWithCrcResult : ShrineUpdateResultWithProgress
+ {
+ public ShrineBreakdown Breakdowns { get; set; }
+ public ShrineResultObfuscatingParameters ObfuscatingParameters { get; set; }
+ public int Count { get; set; }
+ }
+
+ public class ShrineBreakdown
+ {
+ public object[] Counts { get; set; }
+ }
+}
+
diff --git a/src/server/Model/Integration/Shrine/ShrineUpdateResultWithProgress.cs b/src/server/Model/Integration/Shrine/ShrineUpdateResultWithProgress.cs
new file mode 100644
index 000000000..cf40bdf65
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/ShrineUpdateResultWithProgress.cs
@@ -0,0 +1,20 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+namespace Model.Integration.Shrine
+{
+ public class ShrineUpdateResultWithProgress
+ {
+ public long QueryId { get; set; }
+ public string AdapterNodeKey { get; set; }
+ public ShrineQueryStatus Status { get; set; }
+ public string StatusMessage { get; set; }
+ public long? CrcQueryInstanceId { get; set; }
+ public DateTime AdapterTime { get; set; }
+ public ShrineQueryStatusType EncodedClass { get; set; }
+ }
+}
+
diff --git a/src/server/Model/Integration/Shrine/ShrineVersionInfo.cs b/src/server/Model/Integration/Shrine/ShrineVersionInfo.cs
new file mode 100644
index 000000000..8aced911c
--- /dev/null
+++ b/src/server/Model/Integration/Shrine/ShrineVersionInfo.cs
@@ -0,0 +1,18 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+namespace Model.Integration.Shrine
+{
+ public class ShrineVersionInfo
+ {
+ public int ProtocolVersion { get; set; }
+ public int ItemVersion { get; set; }
+ public string ShrineVersion { get; set; }
+ public DateTime CreateDate { get; set; }
+ public DateTime ChangeDate { get; set; }
+ }
+}
+
diff --git a/src/server/Model/Model.csproj b/src/server/Model/Model.csproj
index 2090fb0ad..82a30f7cd 100644
--- a/src/server/Model/Model.csproj
+++ b/src/server/Model/Model.csproj
@@ -18,6 +18,9 @@
+
+
+
@@ -27,6 +30,9 @@
+
+
+
diff --git a/src/server/Model/Options/IntegrationOptions.cs b/src/server/Model/Options/IntegrationOptions.cs
new file mode 100644
index 000000000..f471b9346
--- /dev/null
+++ b/src/server/Model/Options/IntegrationOptions.cs
@@ -0,0 +1,46 @@
+// Copyright (c) 2023, UW Medicine Research IT, University of Washington
+// Developed by Nic Dobbins and Cliff Spital, CRIO Sean Mooney
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+using System;
+
+namespace Model.Options
+{
+ public class IntegrationOptions
+ {
+ public bool Enabled { get; set; } = false;
+ public ShrineIntegrationOptions SHRINE { get; set; }
+ }
+
+ public class ShrineIntegrationOptions : IEnabled
+ {
+ public bool Enabled { get; set; } = false;
+ public string HubApiURI { get; set; }
+ public LocalNode Node { get; set; }
+ public LocalResearcher Researcher { get; set; }
+ public DefaultTopic Topic { get; set; }
+
+ public class LocalNode
+ {
+ public long Id { get; set; }
+ public string Key { get; set; }
+ public string Name { get; set; }
+ }
+
+ public class LocalResearcher
+ {
+ public long Id { get; set; }
+ public string Name { get; set; }
+ public string Domain { get; set; }
+ }
+
+ public class DefaultTopic
+ {
+ public long Id { get; set; }
+ public string Name { get; set; }
+ public string Description { get; set; }
+ }
+ }
+}
+
diff --git a/src/server/Model/Search/PreflightResourceChecker.cs b/src/server/Model/Search/PreflightResourceChecker.cs
index 31be10b4f..dc1c24cfe 100644
--- a/src/server/Model/Search/PreflightResourceChecker.cs
+++ b/src/server/Model/Search/PreflightResourceChecker.cs
@@ -42,11 +42,11 @@ public interface IPreflightConceptReader
public PreflightResourceChecker(
IPreflightResourceReader reader,
- IUserContext user,
+ IUserContextProvider userContextProvider,
ILogger log)
{
this.reader = reader;
- this.user = user;
+ this.user = userContextProvider.GetUserContext();
this.log = log;
}
diff --git a/src/server/Model/Search/QueryManager.cs b/src/server/Model/Search/QueryManager.cs
index fa2be717e..d968a86aa 100644
--- a/src/server/Model/Search/QueryManager.cs
+++ b/src/server/Model/Search/QueryManager.cs
@@ -12,7 +12,6 @@
using Model.Authorization;
using Model.Compiler;
using Model.Extensions;
-using Model.Search;
using Model.Tagging;
using Model.Error;
using System.Data.Common;
diff --git a/src/server/Services/Admin/Compiler/AdminConceptEventService.cs b/src/server/Services/Admin/Compiler/AdminConceptEventService.cs
index fd0cf2628..22cdd148e 100644
--- a/src/server/Services/Admin/Compiler/AdminConceptEventService.cs
+++ b/src/server/Services/Admin/Compiler/AdminConceptEventService.cs
@@ -6,14 +6,11 @@
using System;
using System.Collections.Generic;
using System.Threading.Tasks;
-using Model.Admin;
-using Microsoft.Extensions.Logging;
using Microsoft.Extensions.Options;
using Model.Options;
using System.Data.SqlClient;
using System.Data;
using Dapper;
-using Model.Error;
using Model.Authorization;
using Model.Admin.Compiler;
@@ -26,10 +23,10 @@ public class AdminConceptEventService : AdminConceptEventManager.IAdminConceptEv
public AdminConceptEventService(
IOptions options,
- IUserContext userContext)
+ IUserContext user)
{
opts = options.Value;
- user = userContext;
+ this.user = user;
}
public async Task CreateAsync(ConceptEvent ev)
diff --git a/src/server/Services/Admin/Compiler/AdminConceptService.cs b/src/server/Services/Admin/Compiler/AdminConceptService.cs
index 55a2c6805..ad75183dc 100644
--- a/src/server/Services/Admin/Compiler/AdminConceptService.cs
+++ b/src/server/Services/Admin/Compiler/AdminConceptService.cs
@@ -10,11 +10,8 @@
using System.Linq;
using System.Threading.Tasks;
using Dapper;
-using Microsoft.Extensions.Logging;
using Microsoft.Extensions.Options;
-using Model.Admin;
using Model.Authorization;
-using Model.Error;
using Model.Options;
using Model.Tagging;
using Services.Search;
@@ -30,10 +27,10 @@ public class AdminConceptService : AdminConceptManager.IAdminConceptService
public AdminConceptService(
IOptions options,
- IUserContext userContext)
+ IUserContext user)
{
opts = options.Value;
- user = userContext;
+ this.user = user;
}
public async Task CreateAsync(AdminConcept c)
diff --git a/src/server/Services/Admin/Compiler/AdminConceptSqlSetService.cs b/src/server/Services/Admin/Compiler/AdminConceptSqlSetService.cs
index 4f77d6fa8..d713b3a4f 100644
--- a/src/server/Services/Admin/Compiler/AdminConceptSqlSetService.cs
+++ b/src/server/Services/Admin/Compiler/AdminConceptSqlSetService.cs
@@ -28,11 +28,11 @@ public class AdminConceptSqlSetService : AdminConceptSqlSetManager.IAdminConcept
public AdminConceptSqlSetService(
ILogger logger,
IOptions options,
- IUserContext userContext)
+ IUserContext user)
{
this.logger = logger;
opts = options.Value;
- user = userContext;
+ this.user = user;
}
public async Task CreateAsync(ConceptSqlSet set)
diff --git a/src/server/Services/Admin/Compiler/AdminDatasetCategoryService.cs b/src/server/Services/Admin/Compiler/AdminDatasetCategoryService.cs
index fdf876831..0a4d81837 100644
--- a/src/server/Services/Admin/Compiler/AdminDatasetCategoryService.cs
+++ b/src/server/Services/Admin/Compiler/AdminDatasetCategoryService.cs
@@ -9,16 +9,11 @@
using System.Data.SqlClient;
using System.Data;
using Model.Options;
-using Model.Error;
using Model.Admin.Compiler;
using Model.Authorization;
-using Model.Tagging;
using System.Threading.Tasks;
using Microsoft.Extensions.Options;
using Dapper;
-using Model.Compiler;
-using Services.Tables;
-using Model.Extensions;
namespace Services.Admin.Compiler
{
@@ -28,10 +23,10 @@ public class AdminDatasetCategoryService : AdminDatasetCategoryManager.IAdminDat
readonly AppDbOptions opts;
public AdminDatasetCategoryService(
- IUserContext userContext,
+ IUserContext user,
IOptions opts)
{
- this.user = userContext;
+ this.user = user;
this.opts = opts.Value;
}
diff --git a/src/server/Services/Admin/Compiler/AdminDatasetQueryService.cs b/src/server/Services/Admin/Compiler/AdminDatasetQueryService.cs
index a096769fd..d5c284f25 100644
--- a/src/server/Services/Admin/Compiler/AdminDatasetQueryService.cs
+++ b/src/server/Services/Admin/Compiler/AdminDatasetQueryService.cs
@@ -9,7 +9,6 @@
using System.Data.SqlClient;
using System.Data;
using Model.Options;
-using Model.Error;
using Model.Admin.Compiler;
using Model.Authorization;
using Model.Tagging;
@@ -18,7 +17,6 @@
using Dapper;
using Model.Compiler;
using Services.Tables;
-using Model.Extensions;
using Services.Search;
namespace Services.Admin.Compiler
@@ -28,10 +26,10 @@ public class AdminDatasetQueryService : AdminDatasetQueryManager.IAdminDatasetQu
readonly AppDbOptions opts;
readonly IUserContext user;
- public AdminDatasetQueryService(IOptions opts, IUserContext userContext)
+ public AdminDatasetQueryService(IOptions opts, IUserContext user)
{
this.opts = opts.Value;
- this.user = userContext;
+ this.user = user;
}
public async Task GetDatasetQueryByIdAsync(Guid id)
diff --git a/src/server/Services/Admin/Compiler/AdminDemographicQueryService.cs b/src/server/Services/Admin/Compiler/AdminDemographicQueryService.cs
index f7cfaf925..a66a93663 100644
--- a/src/server/Services/Admin/Compiler/AdminDemographicQueryService.cs
+++ b/src/server/Services/Admin/Compiler/AdminDemographicQueryService.cs
@@ -5,20 +5,14 @@
// file, You can obtain one at http://mozilla.org/MPL/2.0/.
using System;
using System.Collections.Generic;
-using System.Linq;
using System.Data.SqlClient;
using System.Data;
using Model.Options;
-using Model.Error;
using Model.Admin.Compiler;
using Model.Authorization;
-using Model.Tagging;
using System.Threading.Tasks;
using Microsoft.Extensions.Options;
using Dapper;
-using Model.Compiler;
-using Services.Tables;
-using Model.Extensions;
using Services.Search;
namespace Services.Admin.Compiler
@@ -28,10 +22,10 @@ public class AdminDemographicQueryService : AdminDemographicsManager.IAdminDemog
readonly AppDbOptions opts;
readonly IUserContext user;
- public AdminDemographicQueryService(IOptions opts, IUserContext userContext)
+ public AdminDemographicQueryService(IOptions opts, IUserContext user)
{
this.opts = opts.Value;
- this.user = userContext;
+ this.user = user;
}
public async Task GetDemographicQueryAsync()
diff --git a/src/server/Services/Admin/Compiler/AdminGlobalPanelFilterService.cs b/src/server/Services/Admin/Compiler/AdminGlobalPanelFilterService.cs
index a4dbce05c..93647c4d4 100644
--- a/src/server/Services/Admin/Compiler/AdminGlobalPanelFilterService.cs
+++ b/src/server/Services/Admin/Compiler/AdminGlobalPanelFilterService.cs
@@ -21,10 +21,10 @@ public class AdminGlobalPanelFilterService : AdminGlobalPanelFilterManager.IAdmi
readonly AppDbOptions opts;
readonly IUserContext user;
- public AdminGlobalPanelFilterService(IOptions opts, IUserContext userContext)
+ public AdminGlobalPanelFilterService(IOptions opts, IUserContext user)
{
this.opts = opts.Value;
- this.user = userContext;
+ this.user = user;
}
public async Task> GetAsync()
diff --git a/src/server/Services/Admin/Compiler/AdminSpecializationService.cs b/src/server/Services/Admin/Compiler/AdminSpecializationService.cs
index de439d877..c57b308dc 100644
--- a/src/server/Services/Admin/Compiler/AdminSpecializationService.cs
+++ b/src/server/Services/Admin/Compiler/AdminSpecializationService.cs
@@ -6,15 +6,12 @@
using System;
using System.Collections.Generic;
using System.Threading.Tasks;
-using Model.Admin;
using Model.Tagging;
-using Microsoft.Extensions.Logging;
using Microsoft.Extensions.Options;
using Model.Options;
using System.Data.SqlClient;
using System.Data;
using Dapper;
-using Model.Error;
using System.Linq;
using Model.Authorization;
using Model.Admin.Compiler;
@@ -28,10 +25,10 @@ public class AdminSpecializationService : AdminSpecializationManager.IAdminSpeci
public AdminSpecializationService(
IOptions options,
- IUserContext userContext)
+ IUserContext user)
{
opts = options.Value;
- user = userContext;
+ this.user = user;
}
public async Task CreateAsync(Specialization spec)
diff --git a/src/server/Services/Admin/Notification/ServerStateService.cs b/src/server/Services/Admin/Notification/ServerStateService.cs
index 52aa32210..922b939b4 100644
--- a/src/server/Services/Admin/Notification/ServerStateService.cs
+++ b/src/server/Services/Admin/Notification/ServerStateService.cs
@@ -22,10 +22,10 @@ public class AdminServerStateService : AdminServerStateManager.IAdminServerState
readonly AppDbOptions opts;
readonly IUserContext user;
- public AdminServerStateService(IOptions opts, IUserContext userContext)
+ public AdminServerStateService(IOptions opts, IUserContext user)
{
this.opts = opts.Value;
- this.user = userContext;
+ this.user = user;
}
public async Task GetServerStateAsync()
diff --git a/src/server/Services/Cohort/CachedCohortFetcher.cs b/src/server/Services/Cohort/CachedCohortFetcher.cs
index 3d3b6ce9c..77bd2fa0c 100644
--- a/src/server/Services/Cohort/CachedCohortFetcher.cs
+++ b/src/server/Services/Cohort/CachedCohortFetcher.cs
@@ -24,10 +24,10 @@ public class CachedCohortFetcher : ICachedCohortFetcher
readonly AppDbOptions dbOptions;
readonly IUserContext user;
- public CachedCohortFetcher(IOptions dbOptions, IUserContext user)
+ public CachedCohortFetcher(IOptions dbOptions, IUserContextProvider userContextProvider)
{
this.dbOptions = dbOptions.Value;
- this.user = user;
+ this.user = userContextProvider.GetUserContext();
}
public async Task> FetchCohortAsync(Guid queryId, bool exportedOnly)
diff --git a/src/server/Services/Cohort/CohortCacheService.cs b/src/server/Services/Cohort/CohortCacheService.cs
index 426d29ee3..b345bd345 100644
--- a/src/server/Services/Cohort/CohortCacheService.cs
+++ b/src/server/Services/Cohort/CohortCacheService.cs
@@ -70,7 +70,7 @@ ILogger logger
}
var cohortTable = new PatientCohortTable(queryId, cohort.SeasonedPatients(exportLimit, queryId));
- rowCount = cohortTable.Rows.Count();
+ rowCount = cohortTable.Rows.Length;
using (var bc = new SqlBulkCopy(cn))
{
diff --git a/src/server/Services/Cohort/CtePatientCohortService.cs b/src/server/Services/Cohort/CtePatientCohortService.cs
index f041b5a11..8ee56d9a0 100644
--- a/src/server/Services/Cohort/CtePatientCohortService.cs
+++ b/src/server/Services/Cohort/CtePatientCohortService.cs
@@ -35,7 +35,7 @@ protected override async Task GetCohortAsync(PatientCountQuery qu
return new PatientCohort
{
QueryId = query.QueryId,
- PatientIds = await GetPatientSetAsync(cteQuery, query.DependentQueryIds, token),
+ PatientIds = new HashSet(), //await GetPatientSetAsync(cteQuery, query.DependentQueryIds, token),
SqlStatements = new string[] { cteQuery.SqlStatement },
Panels = query.Panels.Where(p => p.Domain == PanelDomain.Panel)
};
diff --git a/src/server/Services/Export/REDCapExportService.cs b/src/server/Services/Export/REDCapExportService.cs
index faa925cb9..50440fe52 100644
--- a/src/server/Services/Export/REDCapExportService.cs
+++ b/src/server/Services/Export/REDCapExportService.cs
@@ -10,7 +10,6 @@
using Microsoft.Extensions.Options;
using System.Net.Http;
using System.Threading.Tasks;
-using System.Net.Http.Headers;
using Newtonsoft.Json;
using Model.Export;
using Newtonsoft.Json.Serialization;
diff --git a/src/server/Services/Search/ConceptDatasetCompilerContextProvider.cs b/src/server/Services/Search/ConceptDatasetCompilerContextProvider.cs
index 6c44469c6..a96ffb971 100644
--- a/src/server/Services/Search/ConceptDatasetCompilerContextProvider.cs
+++ b/src/server/Services/Search/ConceptDatasetCompilerContextProvider.cs
@@ -33,11 +33,11 @@ public class ConceptDatasetCompilerContextProvider : ConceptDatasetCompilerValid
readonly ILogger log;
public ConceptDatasetCompilerContextProvider(
- IUserContext userContext,
+ IUserContext user,
IOptions options,
ILogger logger)
{
- user = userContext;
+ this.user = user;
opts = options.Value;
log = logger;
}
diff --git a/src/server/Services/Search/ConceptHintSearchService.cs b/src/server/Services/Search/ConceptHintSearchService.cs
index 24fbe8997..6a7d39d64 100644
--- a/src/server/Services/Search/ConceptHintSearchService.cs
+++ b/src/server/Services/Search/ConceptHintSearchService.cs
@@ -28,10 +28,10 @@ public class ConceptHintSearchService : ConceptHintSearcher.IConceptHintSearchSe
readonly AppDbOptions opts;
readonly IUserContext user;
- public ConceptHintSearchService(IOptions dbOptions, IUserContext userContext)
+ public ConceptHintSearchService(IOptions dbOptions, IUserContext user)
{
opts = dbOptions.Value;
- user = userContext;
+ this.user = user;
}
///
diff --git a/src/server/Services/Search/ConceptTreeReader.cs b/src/server/Services/Search/ConceptTreeReader.cs
index e394dc67c..7a6d2510b 100644
--- a/src/server/Services/Search/ConceptTreeReader.cs
+++ b/src/server/Services/Search/ConceptTreeReader.cs
@@ -38,10 +38,10 @@ public class ConceptTreeReader : ConceptTreeSearcher.IConceptTreeReader
readonly AppDbOptions opts;
readonly IUserContext user;
- public ConceptTreeReader(IOptions dbOpts, IUserContext userContext)
+ public ConceptTreeReader(IOptions dbOpts, IUserContext user)
{
opts = dbOpts.Value;
- user = userContext;
+ this.user = user;
}
public async Task GetAsync(Guid id)
diff --git a/src/server/Services/Search/DatasetCompilerContextProvider.cs b/src/server/Services/Search/DatasetCompilerContextProvider.cs
index 5335a5e79..a7a980180 100644
--- a/src/server/Services/Search/DatasetCompilerContextProvider.cs
+++ b/src/server/Services/Search/DatasetCompilerContextProvider.cs
@@ -33,11 +33,11 @@ public class DatasetCompilerContextProvider : DatasetCompilerValidationContextPr
};
public DatasetCompilerContextProvider(
- IUserContext userContext,
+ IUserContext user,
IOptions dbOptions,
ILogger logger)
{
- user = userContext;
+ this.user = user;
log = logger;
opts = dbOptions.Value;
}
diff --git a/src/server/Services/Search/DatasetQueryFetcher.cs b/src/server/Services/Search/DatasetQueryFetcher.cs
index ab31428a7..561a5c422 100644
--- a/src/server/Services/Search/DatasetQueryFetcher.cs
+++ b/src/server/Services/Search/DatasetQueryFetcher.cs
@@ -24,10 +24,10 @@ public class DatasetQueryFetcher : IDatasetQueryFetcher
readonly AppDbOptions opts;
public DatasetQueryFetcher(
- IUserContext userContext,
+ IUserContext user,
IOptions dbOptions)
{
- user = userContext;
+ this.user = user;
opts = dbOptions.Value;
}
diff --git a/src/server/Services/Search/DemographicCompilerContextProvider.cs b/src/server/Services/Search/DemographicCompilerContextProvider.cs
index 656ae4c44..fbba3ac2a 100644
--- a/src/server/Services/Search/DemographicCompilerContextProvider.cs
+++ b/src/server/Services/Search/DemographicCompilerContextProvider.cs
@@ -29,11 +29,11 @@ public class DemographicCompilerContextProvider : DemographicCompilerValidationC
readonly ILogger log;
public DemographicCompilerContextProvider(
- IUserContext userContext,
+ IUserContextProvider userContextProvider,
IOptions options,
ILogger logger)
{
- user = userContext;
+ this.user = userContextProvider.GetUserContext();
opts = options.Value;
log = logger;
}
diff --git a/src/server/Services/Search/PanelDatasetCompilerContextProvider.cs b/src/server/Services/Search/PanelDatasetCompilerContextProvider.cs
index 92508b01f..6c0baddf1 100644
--- a/src/server/Services/Search/PanelDatasetCompilerContextProvider.cs
+++ b/src/server/Services/Search/PanelDatasetCompilerContextProvider.cs
@@ -36,11 +36,11 @@ public class PanelDatasetCompilerContextProvider : PanelDatasetCompilerValidatio
};
public PanelDatasetCompilerContextProvider(
- IUserContext userContext,
+ IUserContext user,
IOptions options,
ILogger logger)
{
- user = userContext;
+ this.user = user;
opts = options.Value;
log = logger;
}
diff --git a/src/server/Services/Search/PreflightResourceReader.cs b/src/server/Services/Search/PreflightResourceReader.cs
index 144494f3a..be0a2854f 100644
--- a/src/server/Services/Search/PreflightResourceReader.cs
+++ b/src/server/Services/Search/PreflightResourceReader.cs
@@ -10,7 +10,6 @@
using System.Linq;
using System.Threading.Tasks;
using Dapper;
-using Microsoft.Extensions.Logging;
using Microsoft.Extensions.Options;
using Model.Authorization;
using Model.Compiler;
@@ -28,10 +27,10 @@ public class PreflightResourceReader : PreflightResourceChecker.IPreflightResour
public PreflightResourceReader(
IOptions options,
- IUserContext userContext)
+ IUserContextProvider userContextProvider)
{
opts = options.Value;
- user = userContext;
+ this.user = userContextProvider.GetUserContext();
}
public async Task GetResourcesByIdsAsync(ResourceRefs refs)
diff --git a/src/server/Services/Search/QueryService.cs b/src/server/Services/Search/QueryService.cs
index 6f0bbb2ee..48e621772 100644
--- a/src/server/Services/Search/QueryService.cs
+++ b/src/server/Services/Search/QueryService.cs
@@ -34,11 +34,11 @@ public class QueryService : IQueryService
readonly AppDbOptions dbOpts;
public QueryService(
- IUserContext userContext,
+ IUserContext user,
IOptions