fix optimizations, add to docs

bmeg · Jan 7, 2025 · e0c8e9b · e0c8e9b
1 parent aba2d71
commit e0c8e9b
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Showing 4 changed files with 113 additions and 50 deletions.
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -27,11 +27,11 @@ jobs:
 
         # Login to Quay.io and build image
         docker login quay.io
-        docker buildx create --use
-        docker buildx build --platform linux/amd64,linux/arm64 -t $REPO:$BRANCH . --push
+        docker build -t $REPO:$BRANCH .
 
+        # Add 'latest' tag to 'main' image
         if [[ $BRANCH == 'main' ]]; then
-          docker buildx build --platform linux/amd64,linux/arm64 -t $REPO:latest . --push
+          docker image tag $REPO:main $REPO:latest
         fi
 
         # Push the tagged image to Quay.io

diff --git a/gql-gen/README.md b/gql-gen/README.md
@@ -35,7 +35,7 @@ Filters only currently supported on the first node that is queried. Ex: specimen
 
 ```
 query($filter: JSON){
-  specimen(filter: $filter first:100){
+  specimen(filter: $filter first:100 offset: 5){
     id
     subject{
       ... on PatientType{
@@ -67,3 +67,51 @@ query($filter: JSON){
       }
 }
 ```
+
+## Query Filters
+
+Queries follow the general structure of the FHIR data model except in places where references exist, the graph DB collects all of the vertex data on that specified reference edge and returns it in one dict.
+
+Filters follow the general structure of including "and" and "or" logical operations with comparators as keys
+
+Current supported comparator statements:
+
+| Operator    | Explanation                    |
+| ----------- | ------------------------------ |
+| "eq", "=",  | equal                          |
+| "neq", "!=" | not equal                      |
+| "lt", "<"   | less than                      |
+| "gt", ">"   | greater than                   |
+| "gte", ">=" | greater than or equal          |
+| "lte", "<=" | less than or equal             |
+| "in"        | value is in the list of values |
+
+Example query using random SNOMED codings:
+
+```
+{
+	"filter": {
+		"and": [
+			{
+				"or": [
+					{
+						"=": {
+							"processing.method.coding.display": "Brief intervention"
+						}
+					},
+					{
+						"=": {
+							"processing.method.coding.display": "Cuboid syndrome"
+						}
+					}
+				]
+			},
+			{
+				">": {
+					"collection.bodySite.concept.coding.code": "261665006"
+				}
+			}
+		]
+	}
+}
+```
diff --git a/gql-gen/graph/collectFields.go b/gql-gen/graph/collectFields.go
@@ -4,13 +4,12 @@ import (
 	"context"
 	"fmt"
 	"os"
+	"reflect"
 
-	"strconv"
 	"strings"
 
 	"github.com/99designs/gqlgen/graphql"
 	"github.com/bmeg/grip/gripql"
-	"github.com/bmeg/grip/gripql/inspect"
 	"github.com/vektah/gqlparser/v2/ast"
 )
 
@@ -38,7 +37,7 @@ func (rt *renderTree) NewElement() string {
 }
 
 func queryBuild(query **gripql.Query, selSet ast.SelectionSet, curElement string, rt *renderTree, parentPath string, currentTree map[string]any) {
-	// Recursively traverses AST and builds grip query, renders field tree
+	// Recursively traverses AST and build grip query, renders field tree
 	for _, s := range selSet {
 		switch sel := s.(type) {
 		case *ast.Field:
@@ -95,7 +94,6 @@ func queryBuild(query **gripql.Query, selSet ast.SelectionSet, curElement string
 
 func (r *queryResolver) GetSelectedFieldsAst(ctx context.Context, sourceType string) ([]any, error) {
 	resctx := graphql.GetFieldContext(ctx)
-
 	rt := &renderTree{
 		rFieldPaths: map[string]renderTreePath{"f0": renderTreePath{path: []string{}, unwindPath: []string{}}},
 		rTree:       map[string]any{},
@@ -124,48 +122,20 @@ func (r *queryResolver) GetSelectedFieldsAst(ctx context.Context, sourceType str
 			if err != nil {
 				return nil, err
 			}
-		} else {
-			return nil, fmt.Errorf("filter is specified but filter not populated in variables")
 		}
 	}
 
-	if first, ok := resctx.Args["first"]; ok {
-		firstPtr, _ := first.(*int)
-		if firstPtr == nil {
-			q = q.Limit(uint32(10))
-		} else {
-			q = q.Limit(uint32(*firstPtr))
-		}
-	}
-	if offset, ok := resctx.Args["offset"]; ok {
-		if offset.(*int) != nil {
-			q = q.Skip(uint32(*offset.(*int)))
-		}
-	}
+	// apply default filters after main filters so that all data can be considered in filter before apply filter statements
+	applyDefaultFilters(&q, resctx.Args)
 
 	if os.Getenv("AUTH_ENABLED") == "true" {
 		authList, ok := ctx.Value("auth_list").([]interface{})
 		if !ok {
 			return nil, fmt.Errorf("auth_list not found or invalid")
 		}
-
-		Has_Statement := &gripql.GraphStatement{Statement: &gripql.GraphStatement_Has{gripql.Within("auth_resource_path", authList...)}}
-		steps := inspect.PipelineSteps(q.Statements)
-		FilteredGS := []*gripql.GraphStatement{}
-		for i, v := range q.Statements {
-			steps_index, _ := strconv.Atoi(steps[i])
-			if i == 0 {
-				FilteredGS = append(FilteredGS, v)
-				continue
-			} else if i == steps_index {
-				FilteredGS = append(FilteredGS, v, Has_Statement)
-			} else {
-				FilteredGS = append(FilteredGS, v)
-			}
-		}
-
-		q.Statements = FilteredGS
+		applyAuthFilters(q, authList)
 	}
+
 	q = q.Render(render)
 	fmt.Println("QUERY AFTER RENDER: ", q)
 
@@ -174,19 +144,19 @@ func (r *queryResolver) GetSelectedFieldsAst(ctx context.Context, sourceType str
 		return nil, fmt.Errorf("Traversal Error: %s", err)
 	}
 
-	cachedTree := make(map[string]any, len(rt.rTree))
-	buildTreeStructure(cachedTree, rt.rTree)
+	// Build response tree once, traverse/populate it len(result) times
+	responseTree := make(map[string]any, len(rt.rTree))
+	buildResponseTree(responseTree, rt.rTree)
 
 	out := []any{}
 	for r := range result {
-		values := r.GetRender().GetStructValue().AsMap()
-		data := buildFilteredResponseTree(cachedTree, values)
-		out = append(out, data)
+		out = append(out, populateResponseTree(responseTree, r.GetRender().GetStructValue().AsMap()))
 	}
 	return out, nil
 }
 
-func buildTreeStructure(output map[string]any, renderTree map[string]any) {
+func buildResponseTree(output map[string]any, renderTree map[string]any) {
+	/* Build the skeleton of the response tree without filling in the values */
 	for key, val := range renderTree {
 		switch v := val.(type) {
 		case renderTreePath:
@@ -208,7 +178,7 @@ func buildTreeStructure(output map[string]any, renderTree map[string]any) {
 			}
 		case map[string]any:
 			subTree := make(map[string]any)
-			buildTreeStructure(subTree, v)
+			buildResponseTree(subTree, v)
 			output[key] = subTree
 		case string:
 			if key == "__typename" {
@@ -222,17 +192,24 @@ func buildTreeStructure(output map[string]any, renderTree map[string]any) {
 	}
 }
 
-func buildFilteredResponseTree(cachedTree, values map[string]any) map[string]any {
+func populateResponseTree(cachedTree, values map[string]any) map[string]any {
+	/* fill in the values of the given response tree */
 	output := make(map[string]any, len(cachedTree))
 	for key, val := range cachedTree {
 		switch v := val.(type) {
 		case map[string]any:
-			if filteredSubTree := buildFilteredResponseTree(v, values); len(filteredSubTree) > 0 {
+			if filteredSubTree := populateResponseTree(v, values); len(filteredSubTree) > 0 {
 				output[key] = filteredSubTree
 			}
 		case nil:
 			if renderedValue, exists := values[key+"_data"]; exists {
-				output[key] = renderedValue
+				if reflect.TypeOf(renderedValue) == reflect.TypeOf("") && strings.HasPrefix(renderedValue.(string), "$f") {
+					output[key] = nil
+				} else {
+					output[key] = renderedValue
+				}
+			} else {
+				output[key] = nil
 			}
 		default:
 			output[key] = val

diff --git a/gql-gen/graph/filters.go b/gql-gen/graph/filters.go
@@ -4,10 +4,48 @@ import (
 	"fmt"
 	"strings"
 
+	"strconv"
+
+	"github.com/bmeg/grip/gripql/inspect"
+
 	"github.com/bmeg/grip/gripql"
 	"google.golang.org/protobuf/types/known/structpb"
 )
 
+func applyAuthFilters(q *gripql.Query, authList []any) {
+	Has_Statement := &gripql.GraphStatement{Statement: &gripql.GraphStatement_Has{gripql.Within("auth_resource_path", authList...)}}
+	steps := inspect.PipelineSteps(q.Statements)
+	FilteredGS := []*gripql.GraphStatement{}
+	for i, v := range q.Statements {
+		steps_index, _ := strconv.Atoi(steps[i])
+		if i == 0 {
+			FilteredGS = append(FilteredGS, v)
+			continue
+		} else if i == steps_index {
+			FilteredGS = append(FilteredGS, v, Has_Statement)
+		} else {
+			FilteredGS = append(FilteredGS, v)
+		}
+	}
+	q.Statements = FilteredGS
+}
+
+func applyDefaultFilters(q **gripql.Query, args map[string]any) {
+	if first, ok := args["first"]; ok {
+		firstPtr, _ := first.(*int)
+		if firstPtr == nil {
+			*q = (*q).Limit(uint32(10))
+		} else {
+			*q = (*q).Limit(uint32(*firstPtr))
+		}
+	}
+	if offset, ok := args["offset"]; ok {
+		if offset.(*int) != nil {
+			*q = (*q).Skip(uint32(*offset.(*int)))
+		}
+	}
+}
+
 func (rt *renderTree) applyUnwinds(query **gripql.Query) {
 	/* Assumes query is at f0 and only applies unwinds to that node currently*/
 	for _, val := range rt.rFieldPaths["f0"].unwindPath {