working medical history pagination
- performance improvements by using placeholder ids for graph - only inflating with real resources once we've calculated pagination window.
This commit is contained in:
Jason Kulatunga
parent
21dc5ebe92
commit
345b2d5cfd
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@ -141,7 +141,8 @@ func (sr *SqliteRepository) GetUserByUsername(ctx context.Context, username stri
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return &foundUser, result.Error
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}
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// TODO: check for error, right now we return a nil which may cause a panic.
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//TODO: check for error, right now we return a nil which may cause a panic.
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//TODO: can we cache the current user? //SECURITY:
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func (sr *SqliteRepository) GetCurrentUser(ctx context.Context) (*models.User, error) {
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username := ctx.Value(pkg.ContextKeyTypeAuthUsername)
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if username == nil {
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@ -446,6 +447,7 @@ func (sr *SqliteRepository) ListResources(ctx context.Context, queryOptions mode
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}
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}
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//TODO: should this be deprecated? (replaced by ListResources)
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func (sr *SqliteRepository) GetResourceByResourceTypeAndId(ctx context.Context, sourceResourceType string, sourceResourceId string) (*models.ResourceBase, error) {
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currentUser, currentUserErr := sr.GetCurrentUser(ctx)
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if currentUserErr != nil {
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@ -635,14 +637,13 @@ func (sr *SqliteRepository) FindResourceAssociationsByTypeAndId(ctx context.Cont
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// - find source for each resource
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// - (SECURITY) ensure the current user and the source for each resource matches
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// - check if there is a Composition resource Type already.
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// - if Composition type already exists:
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// - update "relatesTo" field with additional data.
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// - else:
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// - Create a Composition resource type (populated with "relatesTo" references to all provided Resources)
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//
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// - if Composition type already exists:
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// - update "relatesTo" field with additional data.
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// - else:
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// - Create a Composition resource type (populated with "relatesTo" references to all provided Resources)
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// - add AddResourceAssociation for all resources linked to the Composition resource
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// - store the Composition resource
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// TODO: determine if we should be using a List Resource instead of a Composition resource
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//TODO: determine if we should be using a List Resource instead of a Composition resource
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func (sr *SqliteRepository) AddResourceComposition(ctx context.Context, compositionTitle string, resources []*models.ResourceBase) error {
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currentUser, currentUserErr := sr.GetCurrentUser(ctx)
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if currentUserErr != nil {
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@ -7,6 +7,7 @@ import (
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"github.com/fastenhealth/fasten-onprem/backend/pkg"
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"github.com/fastenhealth/fasten-onprem/backend/pkg/models"
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"github.com/fastenhealth/fasten-onprem/backend/pkg/utils"
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databaseModel "github.com/fastenhealth/fasten-onprem/backend/pkg/models/database"
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"golang.org/x/exp/slices"
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"log"
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"strings"
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@ -89,7 +90,9 @@ func (sr *SqliteRepository) GetFlattenedResourceGraph(ctx context.Context, graph
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}
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}
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for _, resourcePlaceholder := range resourcePlaceholders {
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for ndx, _ := range resourcePlaceholders {
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resourcePlaceholder := resourcePlaceholders[ndx]
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log.Printf("Adding vertex: %v", resourcePlaceholder.ID())
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err := g.AddVertex(
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&resourcePlaceholder,
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)
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@ -187,74 +190,153 @@ func (sr *SqliteRepository) GetFlattenedResourceGraph(ctx context.Context, graph
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resourcePlaceholderListDictionary[foundSourceType] = append(resourcePlaceholderListDictionary[foundSourceType], resourcePlaceholder)
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}
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// Step 2: define a function. When given a resource, should find all related resources, flatten the heirarchy and set the RelatedResourceFhir list
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flattenRelatedResourcesFn := func(resourcePlaceholder *VertexResourcePlaceholder) {
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// Step 2: now that we've created a relationship graph using placeholders, we need to determine which page of resources to return
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// and look up the actual resources from the database.
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resourceListDictionary, err := sr.InflateResourceGraphAtPage(resourcePlaceholderListDictionary, options.Page)
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if err != nil {
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return nil, fmt.Errorf("error while paginating & inflating resource graph: %v", err)
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}
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// Step 3: define a function. When given a resource, should find all related resources, flatten the heirarchy and set the RelatedResourceFhir list
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flattenRelatedResourcesFn := func(resource *models.ResourceBase) {
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// this is a "root" encounter, which is not related to any condition, we should add it to the Unknown encounters list
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vertexId := resourceVertexId(resourcePlaceholder)
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vertexId := resourceVertexId(&VertexResourcePlaceholder{
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ResourceType: resource.SourceResourceType,
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ResourceID: resource.SourceResourceID,
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SourceID: resource.SourceID.String(),
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UserID: resource.UserID.String(),
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})
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sr.Logger.Debugf("populating resourcePlaceholder: %s", vertexId)
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resourcePlaceholder.RelatedResourcePlaceholder = []*VertexResourcePlaceholder{}
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resource.RelatedResource = []*models.ResourceBase{}
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//get all the resources associated with this node
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//get all the resource placeholders associated with this node
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//TODO: handle error?
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graph.DFS(g, vertexId, func(relatedVertexId string) bool {
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relatedResourcePlaceholder, _ := g.Vertex(relatedVertexId)
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//skip the current resourcePlaceholder if it's referenced in this list.
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//also skip the current resourcePlaceholder if its a Binary resourcePlaceholder (which is a special case)
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if vertexId != resourceVertexId(relatedResourcePlaceholder) && relatedResourcePlaceholder.ResourceType != "Binary" {
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resourcePlaceholder.RelatedResourcePlaceholder = append(resourcePlaceholder.RelatedResourcePlaceholder, relatedResourcePlaceholder)
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relatedResource, err := sr.GetResourceByResourceTypeAndId(ctx, relatedResourcePlaceholder.ResourceType, relatedResourcePlaceholder.ResourceID)
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if err != nil {
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sr.Logger.Warnf("ignoring, cannot safely handle error which occurred while getting related resource: %v", err)
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return true
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}
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resource.RelatedResource = append(
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resource.RelatedResource,
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relatedResource,
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)
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}
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return false
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})
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}
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// Step 3: now that we've created a relationship graph using placeholders, we need to determine which page of resources to return
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// and look up the actual resources from the database.
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//TODO: Step 3a: since we cant calulate the sort order until the resources are loaded, we need to load all the root resources first.
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// Step 4: flatten resources (if needed) and sort them
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for resourceType, _ := range resourcePlaceholderListDictionary {
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for resourceType, _ := range resourceListDictionary {
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sourceFlatten, sourceFlattenOk := sourceFlattenLevel[strings.ToLower(resourceType)]
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if sourceFlattenOk && sourceFlatten == true {
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//if flatten is set to true, we want to flatten the graph. This is usually for non primary source types (eg. Encounter is a source type, but Condition is the primary source type)
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// Step 3: populate related resources for each encounter, flattened
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for ndx, _ := range resourcePlaceholderListDictionary[resourceType] {
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for ndx, _ := range resourceListDictionary[resourceType] {
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// this is a "root" encounter, which is not related to any condition, we should add it to the Unknown encounters list
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flattenRelatedResourcesFn(resourcePlaceholderListDictionary[resourceType][ndx])
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flattenRelatedResourcesFn(resourceListDictionary[resourceType][ndx])
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//sort all related resources (by date, desc)
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resourcePlaceholderListDictionary[resourceType][ndx].RelatedResource = utils.SortResourcePtrListByDate(resourcePlaceholderListDictionary[resourceType][ndx].RelatedResource)
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resourceListDictionary[resourceType][ndx].RelatedResource = utils.SortResourcePtrListByDate(resourceListDictionary[resourceType][ndx].RelatedResource)
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}
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} else {
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// if flatten is set to false, we want to preserve the top relationships in the graph heirarchy. This is usually for primary source types (eg. Condition is the primary source type)
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// we want to ensure context is preserved, so we will flatten the graph futher down in the heirarchy
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// Step 4: find all encounters referenced by the root conditions, populate them, then add them to the condition as RelatedResourceFhir
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for ndx, _ := range resourcePlaceholderListDictionary[resourceType] {
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for ndx, _ := range resourceListDictionary[resourceType] {
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// this is a "root" condition,
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resourcePlaceholderListDictionary[resourceType][ndx].RelatedResource = []*models.ResourceBase{}
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vertexId := resourceVertexId(resourcePlaceholderListDictionary[resourceType][ndx])
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resourceListDictionary[resourceType][ndx].RelatedResource = []*models.ResourceBase{}
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currentResource := resourceListDictionary[resourceType][ndx]
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vertexId := resourceKeysVertexId(currentResource.SourceID.String(), currentResource.SourceResourceType, currentResource.SourceResourceID)
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for relatedVertexId, _ := range adjacencyMap[vertexId] {
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relatedResourceFhir, _ := g.Vertex(relatedVertexId)
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relatedResourcePlaceholder, _ := g.Vertex(relatedVertexId)
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relatedResourceFhir, err := sr.GetResourceByResourceTypeAndId(ctx, relatedResourcePlaceholder.ResourceType, relatedResourcePlaceholder.ResourceID)
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if err != nil {
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sr.Logger.Warnf("ignoring, cannot safely handle error which occurred while getting related resource (flatten=false): %v", err)
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continue
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}
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flattenRelatedResourcesFn(relatedResourceFhir)
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resourcePlaceholderListDictionary[resourceType][ndx].RelatedResource = append(resourcePlaceholderListDictionary[resourceType][ndx].RelatedResource, relatedResourceFhir)
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resourceListDictionary[resourceType][ndx].RelatedResource = append(resourceListDictionary[resourceType][ndx].RelatedResource, relatedResourceFhir)
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}
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//sort all related resources (by date, desc)
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resourcePlaceholderListDictionary[resourceType][ndx].RelatedResource = utils.SortResourcePtrListByDate(resourcePlaceholderListDictionary[resourceType][ndx].RelatedResource)
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resourceListDictionary[resourceType][ndx].RelatedResource = utils.SortResourcePtrListByDate(resourceListDictionary[resourceType][ndx].RelatedResource)
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}
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}
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resourcePlaceholderListDictionary[resourceType] = utils.SortResourcePtrListByDate(resourcePlaceholderListDictionary[resourceType])
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resourceListDictionary[resourceType] = utils.SortResourcePtrListByDate(resourceListDictionary[resourceType])
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}
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// Step 5: return the populated resource list dictionary
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return resourcePlaceholderListDictionary, nil
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return resourceListDictionary, nil
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}
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// LoadResourceGraphAtPage - this function will take a dictionary of placeholder "sources" graph and load the actual resources from the database, for a specific page
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// - first, it will load all the "source" resources (eg. Encounter, Condition, etc)
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// - sort the root resources by date, desc
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// - use the page number + page size to determine which root resources to return
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// - return a dictionary of "source" resource lists
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func (sr *SqliteRepository) InflateResourceGraphAtPage(resourcePlaceholderListDictionary map[string][]*VertexResourcePlaceholder, page int) (map[string][]*models.ResourceBase, error) {
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// Step 3a: since we cant calulate the sort order until the resources are loaded, we need to load all the root resources first.
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//TODO: maybe its more performant to query each resource by type/id/source, since they are indexed already?
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rootWrappedResourceModels := []models.ResourceBase{}
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for resourceType, _ := range resourcePlaceholderListDictionary {
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// resourcePlaceholderListDictionary contains top level resource types (eg. Encounter, Condition, etc)
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selectList := [][]interface{}{}
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for ndx, _ := range resourcePlaceholderListDictionary[resourceType] {
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selectList = append(selectList, []interface{}{
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resourcePlaceholderListDictionary[resourceType][ndx].UserID,
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resourcePlaceholderListDictionary[resourceType][ndx].SourceID,
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resourcePlaceholderListDictionary[resourceType][ndx].ResourceType,
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resourcePlaceholderListDictionary[resourceType][ndx].ResourceID,
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})
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}
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tableName, err := databaseModel.GetTableNameByResourceType(resourceType)
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if err != nil {
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return nil, err
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}
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var tableWrappedResourceModels []models.ResourceBase
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sr.GormClient.
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Where("(user_id, source_id, source_resource_type, source_resource_id) IN ?", selectList).
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Table(tableName).
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Find(&tableWrappedResourceModels)
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//append these resources to the rootWrappedResourceModels list
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rootWrappedResourceModels = append(rootWrappedResourceModels, tableWrappedResourceModels...)
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}
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//sort
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rootWrappedResourceModels = utils.SortResourceListByDate(rootWrappedResourceModels)
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//paginate (by calculating window for the slice)
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rootWrappedResourceModels = utils.PaginateResourceList(rootWrappedResourceModels, page, 20) //todo: replace size with pkg.ResourceListPageSize
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// Step 3b: now that we have the root resources, lets generate a dictionary of resource lists, keyed by resource type
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resourceListDictionary := map[string][]*models.ResourceBase{}
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for ndx, _ := range rootWrappedResourceModels {
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resourceType := rootWrappedResourceModels[ndx].SourceResourceType
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if _, ok := resourceListDictionary[resourceType]; !ok {
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resourceListDictionary[resourceType] = []*models.ResourceBase{}
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}
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resourceListDictionary[resourceType] = append(resourceListDictionary[resourceType], &rootWrappedResourceModels[ndx])
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}
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// Step 4: return the populated resource list dictionary
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return resourceListDictionary, nil
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}
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//We need to support the following types of graphs:
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@ -0,0 +1,16 @@
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package utils
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import "github.com/fastenhealth/fastenhealth-onprem/backend/pkg/models"
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func PaginateResourceList(resourceList []models.ResourceBase, skip int, size int) []models.ResourceBase {
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if skip > len(resourceList) {
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skip = len(resourceList)
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}
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end := skip + size
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if end > len(resourceList) {
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end = len(resourceList)
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}
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return resourceList[skip:end]
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}
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@ -129,7 +129,18 @@ func GetResourceFhirGraph(c *gin.Context) {
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graphType := strings.Trim(c.Param("graphType"), "/")
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resourceListDictionary, err := databaseRepo.GetFlattenedResourceGraph(c, pkg.ResourceGraphType(graphType))
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graphOptions := models.ResourceGraphOptions{}
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if len(c.Query("page")) > 0 {
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pageNumb, err := strconv.Atoi(c.Query("page"))
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if err != nil {
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logger.Errorln("An error occurred while calculating page number", err)
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c.JSON(http.StatusInternalServerError, gin.H{"success": false})
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return
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}
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graphOptions.Page = pageNumb
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}
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resourceListDictionary, err := databaseRepo.GetFlattenedResourceGraph(c, pkg.ResourceGraphType(graphType), graphOptions)
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if err != nil {
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logger.Errorln("An error occurred while retrieving list of resources", err)
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c.JSON(http.StatusInternalServerError, gin.H{"success": false})
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