Merge pull request #118 from molgenis/feat/queryForNull

handle undefined values for has_any any_has_any when not querying for…

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@molgenis/vip-report-api",
-  "version": "6.1.1",
+  "version": "6.1.2",
   "description": "TypeScript Report API for Variant Call Format (VCF) Report Templates",
   "scripts": {
     "build": "tsc --build",

src/__tests__/apiClient.test.ts

@@ -21,7 +21,7 @@ const record0: Item<VcfRecord> = {
     i: [],
     r: "C",
     a: ["T"],
-    q: null,
+    q: 80,
     f: ["PASS"],
     n: {
       n_array0: ["c", null, "d", "b"],
@@ -79,7 +79,7 @@ const record1: Item<VcfRecord> = {
     r: "G",
     a: ["A"],
     q: null,
-    f: ["PASS"],
+    f: [],
     n: {
       n_array0: ["b", "c", "a"],
       n_array1: ["a", "b"],
@@ -393,6 +393,38 @@ test("get - records with less than query", async () => {
   });
 });
 
+test("get - records with equals null query on qual", async () => {
+  const params: Params = {
+    query: {
+      selector: ["q"],
+      operator: "==",
+      args: null,
+    },
+  };
+  const records = await api.getRecords(params);
+  expect(records).toEqual({
+    items: [record1],
+    page: { number: 0, size: 10, totalElements: 1 },
+    total: 2,
+  });
+});
+
+test("get - records with equals empty filter", async () => {
+  const params: Params = {
+    query: {
+      selector: ["f"],
+      operator: "==",
+      args: [],
+    },
+  };
+  const records = await api.getRecords(params);
+  expect(records).toEqual({
+    items: [record1],
+    page: { number: 0, size: 10, totalElements: 1 },
+    total: 2,
+  });
+});
+
 test("get - records with equals null query", async () => {
   const params: Params = {
     query: {
@@ -867,6 +899,22 @@ test("get - some records using has_any undefined", async () => {
   });
 });
 
+test("get - some records using has_any with undefined values", async () => {
+  const params: Params = {
+    query: {
+      selector: ["n", "n_array1"],
+      operator: "has_any",
+      args: ["a"],
+    },
+  };
+  const records = await api.getRecords(params);
+  expect(records).toEqual({
+    items: [record1],
+    page: { number: 0, size: 10, totalElements: 1 },
+    total: 2,
+  });
+});
+
 test("get - some records using has_any null", async () => {
   const params: Params = {
     query: {
@@ -899,6 +947,22 @@ test("get - some records using empty any_has_any", async () => {
   });
 });
 
+test("get - some records using undefined any_has_any value", async () => {
+  const params: Params = {
+    query: {
+      selector: ["n", "n_object0", "*", "5"],
+      operator: "any_has_any",
+      args: ["a"],
+    },
+  };
+  const records = await api.getRecords(params);
+  expect(records).toEqual({
+    items: [],
+    page: { number: 0, size: 10, totalElements: 0 },
+    total: 2,
+  });
+});
+
 test("get - some records using wildcard selector part with !has_any", async () => {
   const params: Params = {
     query: {

src/__tests__/trio.vcf

@@ -16,5 +16,5 @@
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##FORMAT=<ID=VIPC_S,Number=.,Type=String,Description="VIP decision tree classification.">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Patient	Mother	Father
-1	10042538	.	C	T	.	PASS	n_array0=c,,d,b;n_number2=1;n_object0=dummy5|c|1&2,dummy7||1&2,dummy1|d|1&2,dummy4|b|1&2;n_string0=a;n_string3=b;n_string4=b	GT:DP:AD	1|0:50:45,5	0|0:10:10,0	0|0:10:10,0
-1	16376412	.	G	A	.	PASS	n_array0=b,c,a;n_array1=a,b;n_bool3;n_bool6;n_bool7;n_number2=0;n_object0=dummy3|b|1&2&3,dummy2|c|1&2&3,dummy6|a|;n_string0=a;n_string3=a;n_string4=A	GT:DP:AD	0|1:10:0,0	1|0:11:11,0	1|0:11:11,0
+1	10042538	.	C	T	80	PASS	n_array0=c,,d,b;n_number2=1;n_object0=dummy5|c|1&2,dummy7||1&2,dummy1|d|1&2,dummy4|b|1&2;n_string0=a;n_string3=b;n_string4=b	GT:DP:AD	1|0:50:45,5	0|0:10:10,0	0|0:10:10,0
+1	16376412	.	G	A	.	.	n_array0=b,c,a;n_array1=a,b;n_bool3;n_bool6;n_bool7;n_number2=0;n_object0=dummy3|b|1&2&3,dummy2|c|1&2&3,dummy6|a|;n_string0=a;n_string3=a;n_string4=A	GT:DP:AD	0|1:10:0,0	1|0:11:11,0	1|0:11:11,0

src/apiClient.ts

@@ -374,6 +374,16 @@ function matches(query: Query, resource: Item<Resource>): boolean {
 
 function matchesEquals(query: QueryClause, resource: Item<Resource>): boolean {
   const value: unknown = select(query.selector, resource);
+  if (Array.isArray(query.args)) {
+    if (value === undefined || value === null) {
+      return false;
+    }
+    if ((query.args as unknown[]).length === 0) {
+      return (value as unknown[]).length === 0;
+    } else {
+      throw new Error(`Equals query with an array is only supported with an empty array.`);
+    }
+  }
   return value === query.args;
 }
 
@@ -473,20 +483,25 @@ function matchesAnyHasAny(query: QueryClause, resource: Item<Resource>): boolean
         }
       }
     }
-  } else if ((query.args as unknown[]).length === 0) {
-    for (const item of value as unknown[]) {
-      if ((item as unknown[]).length === 0) {
-        match = true;
-        break;
-      }
-    }
   } else {
-    for (const item of value as unknown[]) {
-      if (item !== null) {
-        for (const arg of query.args as unknown[]) {
-          if ((item as unknown[]).includes(arg)) {
-            match = true;
-            break;
+    if (value === undefined) {
+      return false;
+    }
+    if ((query.args as unknown[]).length === 0) {
+      for (const item of value as unknown[]) {
+        if ((item as unknown[]).length === 0) {
+          match = true;
+          break;
+        }
+      }
+    } else {
+      for (const item of value as unknown[]) {
+        if (item !== null) {
+          for (const arg of query.args as unknown[]) {
+            if (item !== undefined && (item as unknown[]).includes(arg)) {
+              match = true;
+              break;
+            }
           }
         }
       }
@@ -514,6 +529,9 @@ function matchesHasAny(query: QueryClause, resource: Item<Resource>): boolean {
       }
     }
   } else {
+    if (value === undefined) {
+      return false;
+    }
     for (const arg of query.args as unknown[]) {
       if ((value as unknown[]).includes(arg)) {
         match = true;