From 06506d3292131fcf01e4b01f51256e30a1920a7c Mon Sep 17 00:00:00 2001
From: mswertz <m.a.swertz@rug.nl>
Date: Tue, 26 Nov 2024 22:52:09 +0100
Subject: [PATCH 01/16] wip

---
 apps/reports/src/components/ListReports.vue   |  8 ++--
 .../reports/src/components/ViewEditReport.vue | 42 +++++++++++++++----
 apps/reports/src/main.js                      |  2 +-
 .../graphql/GraphqlSchemaFieldFactory.java    | 23 ++++++----
 .../java/org/molgenis/emx2/web/ZipApi.java    | 23 ++++++++--
 5 files changed, 74 insertions(+), 24 deletions(-)

diff --git a/apps/reports/src/components/ListReports.vue b/apps/reports/src/components/ListReports.vue
index e6b74f4fe3..ed1b1d583d 100644
--- a/apps/reports/src/components/ListReports.vue
+++ b/apps/reports/src/components/ListReports.vue
@@ -32,7 +32,7 @@
       >
       <TableSimple
         @rowClick="open"
-        :columns="['id', 'name']"
+        :columns="['index', 'id', 'name']"
         :rows="reportsWithId"
         class="bg-white"
         selectColumn="id"
@@ -42,6 +42,7 @@
           <IconAction v-if="canEdit" icon="plus" @click="add" />
         </template>
         <template v-slot:rowheader="slotProps">
+          {{ slotProps.row }}
           <IconAction
             v-if="canEdit"
             icon="pencil-alt"
@@ -101,7 +102,8 @@ export default {
       if (this.reports) {
         let index = 0;
         return this.reports.map((report) => {
-          report.id = index++;
+          report.index = index++;
+          report.id = report.id || report.index;
           return report;
         });
       }
@@ -116,7 +118,7 @@ export default {
     },
     async add() {
       this.error = null;
-      this.reports.push({ name: "new report", sql: "" });
+      this.reports.push({ id: "newid", name: "new report", sql: "" });
       await this.client
         .saveSetting("reports", this.reports)
         .catch((error) => (this.error = error));
diff --git a/apps/reports/src/components/ViewEditReport.vue b/apps/reports/src/components/ViewEditReport.vue
index e03a784744..9f19ec4486 100644
--- a/apps/reports/src/components/ViewEditReport.vue
+++ b/apps/reports/src/components/ViewEditReport.vue
@@ -1,4 +1,5 @@
 <template>
+  index={{ index }} id={{ id }}
   <Spinner v-if="!session" />
   <MessageWarning
     v-else-if="
@@ -16,7 +17,19 @@
       <h2>
         Edit report: {{ id }}<IconAction icon="eye" @click="edit = false" />
       </h2>
-      <InputString id="reportName" v-model="name" label="name" />
+      <InputString
+        id="reportId"
+        v-model="id"
+        label="id"
+        :required="true"
+        description="unique index"
+      />
+      <InputString
+        id="reportName"
+        v-model="name"
+        label="name"
+        description="human readible label"
+      />
       <InputText
         id="reportSql"
         v-model="sql"
@@ -96,13 +109,14 @@ export default {
   },
   props: {
     session: Object,
-    id: String,
+    index: String,
     limit: { type: Number, default: 5 },
   },
   data() {
     return {
       rows: undefined,
       count: null,
+      id: null,
       sql: 'select * from "Pet"',
       name: null,
       parameters: {},
@@ -175,7 +189,11 @@ export default {
       const offset = this.limit * (this.page - 1);
       const result = await request(
         "graphql",
-        `query report($parameters:[MolgenisSettingsInput]) {_reports(id:${this.id},parameters:$parameters,limit:${this.limit},offset:${offset}){data,count}}`,
+        `query report($parameters:[MolgenisSettingsInput]) {_reports(id:"${
+          this.id || this.index
+        }",parameters:$parameters,limit:${
+          this.limit
+        },offset:${offset}){data,count}}`,
         {
           parameters: this.parameterKeyValueMap,
         }
@@ -186,11 +204,20 @@ export default {
       this.count = result._reports.count;
     },
     async save() {
+      if (this.id == null) {
+        this.error = "id is required";
+        return;
+      }
+      if (this.sql == null) {
+        this.error = "sql is required";
+        return;
+      }
       this.succes = null;
       this.error = null;
       const reports = await this.client.fetchSettingValue("reports");
-      reports[this.id].sql = this.sql;
-      reports[this.id].name = this.name;
+      reports[this.index].id = this.id;
+      reports[this.index].sql = this.sql;
+      reports[this.index].name = this.name;
       this.client
         .saveSetting("reports", reports)
         .then((res) => {
@@ -202,8 +229,9 @@ export default {
     async reload() {
       const reports = await this.client.fetchSettingValue("reports");
       if (reports[this.id]) {
-        this.sql = reports[this.id].sql;
-        this.name = reports[this.id].name;
+        this.id = reports[this.index].id;
+        this.sql = reports[this.index].sql;
+        this.name = reports[this.index].name;
       } else {
         this.error = "report not found";
       }
diff --git a/apps/reports/src/main.js b/apps/reports/src/main.js
index 53aae0a698..8b335cb9cb 100644
--- a/apps/reports/src/main.js
+++ b/apps/reports/src/main.js
@@ -15,7 +15,7 @@ const router = createRouter({
       props: true,
     },
     {
-      path: "/:id",
+      path: "/:index",
       name: "edit",
       component: ViewReport,
       props: true,
diff --git a/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java b/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java
index 1b703a6120..e041f89b21 100644
--- a/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java
+++ b/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java
@@ -13,10 +13,7 @@
 import graphql.Scalars;
 import graphql.schema.*;
 import java.io.IOException;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 import java.util.stream.Stream;
 import org.jooq.JSONB;
 import org.molgenis.emx2.*;
@@ -863,7 +860,7 @@ public GraphQLFieldDefinition schemaReportsField(Schema schema) {
                     GraphQLFieldDefinition.newFieldDefinition()
                         .name(COUNT)
                         .type(Scalars.GraphQLInt)))
-        .argument(GraphQLArgument.newArgument().name(ID).type(Scalars.GraphQLInt))
+        .argument(GraphQLArgument.newArgument().name(ID).type(Scalars.GraphQLString))
         .argument(
             GraphQLArgument.newArgument()
                 .name(PARAMETERS)
@@ -872,20 +869,26 @@ public GraphQLFieldDefinition schemaReportsField(Schema schema) {
         .argument(GraphQLArgument.newArgument().name(OFFSET).type(Scalars.GraphQLInt))
         .dataFetcher(
             dataFetchingEnvironment -> {
-              Integer id = null;
               Map<String, Object> result = new LinkedHashMap<>();
               try {
                 String reportsJson = schema.getMetadata().getSetting("reports");
                 logger.info("REPORT value: " + reportsJson);
                 if (reportsJson != null) {
-                  id = dataFetchingEnvironment.getArgument(ID);
+                  final String id = dataFetchingEnvironment.getArgument(ID);
                   Integer offset = dataFetchingEnvironment.getArgumentOrDefault(OFFSET, 0);
                   Integer limit = dataFetchingEnvironment.getArgumentOrDefault(LIMIT, 10);
                   Map<String, String> parameters =
                       convertKeyValueListToMap(dataFetchingEnvironment.getArgument(PARAMETERS));
                   List<Map<String, Object>> reportList =
                       new ObjectMapper().readValue(reportsJson, List.class);
-                  Map<String, Object> report = reportList.get(id);
+                  Map<String, Object> report =
+                      reportList.stream()
+                          .filter(r -> id.equals(r.get("id")))
+                          .findFirst()
+                          .orElseGet(() -> null);
+                  if (report == null) {
+                    report = reportList.get(Integer.parseInt(id));
+                  }
                   String sql = report.get("sql") + " LIMIT " + limit + " OFFSET " + offset;
                   String countSql =
                       String.format("select count(*) from (%s) as count", report.get("sql"));
@@ -896,7 +899,9 @@ public GraphQLFieldDefinition schemaReportsField(Schema schema) {
                 }
                 return result;
               } catch (Exception e) {
-                throw new MolgenisException("Retrieve of report '" + id + "' failed ", e);
+                throw new MolgenisException(
+                    "Retrieve of report '" + dataFetchingEnvironment.getArgument(ID) + "' failed ",
+                    e);
               }
             })
         .build();
diff --git a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
index ff6d96e127..dcac0857aa 100644
--- a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
+++ b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
@@ -174,16 +174,31 @@ static void getZippedReports(Context ctx) throws IOException {
     }
   }
 
-  static void generateReportsToStore(Context ctx, TableStore store) throws JsonProcessingException {
+  static void generateReportsToStore(
+      @org.jetbrains.annotations.NotNull Context ctx, TableStore store)
+      throws JsonProcessingException {
     String reports = ctx.queryParam("id");
     Schema schema = getSchema(ctx);
     Map<String, ?> parameters = getReportParameters(ctx);
     String reportsJson = schema.getMetadata().getSetting("reports");
     List<Map<String, String>> reportList = new ObjectMapper().readValue(reportsJson, List.class);
     for (String reportId : reports.split(",")) {
-      Map reportObject = reportList.get(Integer.parseInt(reportId));
-      String sql = (String) reportObject.get("sql");
-      String name = (String) reportObject.get("name");
+      // first find report object based on id
+      Optional<Map<String, String>> found =
+          reportList.stream()
+              .filter(reportDefinition -> reportId.equals(reportDefinition.get("id")))
+              .findFirst();
+      Map<String, String> reportObject = null;
+      if (found.isPresent()) {
+        reportObject = found.get();
+      } else {
+        reportObject = reportList.get(Integer.parseInt(reportId));
+      }
+      if (reportObject == null) {
+        throw new MolgenisException("Cannot find report id=" + reportId);
+      }
+      String sql = reportObject.get("sql");
+      String name = reportObject.get("name");
       List<Row> rows = schema.retrieveSql(sql, parameters);
       if (rows.size() > 0) {
         store.writeTable(name, new ArrayList<>(rows.get(0).getColumnNames()), rows);

From 93e9c150eb80e572e232e02f70cf899115b031e8 Mon Sep 17 00:00:00 2001
From: mswertz <m.a.swertz@rug.nl>
Date: Wed, 27 Nov 2024 19:29:19 +0100
Subject: [PATCH 02/16] complete?

---
 apps/reports/src/components/ListReports.vue         |  3 +--
 apps/reports/src/components/ViewEditReport.vue      |  3 +--
 .../main/java/org/molgenis/emx2/web/JsonApi.java    | 13 ++++++++++---
 .../src/main/java/org/molgenis/emx2/web/ZipApi.java |  5 ++---
 4 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/apps/reports/src/components/ListReports.vue b/apps/reports/src/components/ListReports.vue
index ed1b1d583d..586b666a2f 100644
--- a/apps/reports/src/components/ListReports.vue
+++ b/apps/reports/src/components/ListReports.vue
@@ -42,7 +42,6 @@
           <IconAction v-if="canEdit" icon="plus" @click="add" />
         </template>
         <template v-slot:rowheader="slotProps">
-          {{ slotProps.row }}
           <IconAction
             v-if="canEdit"
             icon="pencil-alt"
@@ -133,7 +132,7 @@ export default {
       this.reload();
     },
     open(row) {
-      this.$router.push({ name: "edit", params: { id: row.id } });
+      this.$router.push({ name: "edit", params: { index: row.index } });
     },
     downloadSelected() {
       window.open(
diff --git a/apps/reports/src/components/ViewEditReport.vue b/apps/reports/src/components/ViewEditReport.vue
index 9f19ec4486..0342530b29 100644
--- a/apps/reports/src/components/ViewEditReport.vue
+++ b/apps/reports/src/components/ViewEditReport.vue
@@ -1,5 +1,4 @@
 <template>
-  index={{ index }} id={{ id }}
   <Spinner v-if="!session" />
   <MessageWarning
     v-else-if="
@@ -228,7 +227,7 @@ export default {
     },
     async reload() {
       const reports = await this.client.fetchSettingValue("reports");
-      if (reports[this.id]) {
+      if (reports[this.index]) {
         this.id = reports[this.index].id;
         this.sql = reports[this.index].sql;
         this.name = reports[this.index].name;
diff --git a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/JsonApi.java b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/JsonApi.java
index 662c578768..3e0bc3efff 100644
--- a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/JsonApi.java
+++ b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/JsonApi.java
@@ -37,9 +37,16 @@ public static void getJsonReport(Context ctx) throws JsonProcessingException {
     Map<String, Object> jsonResponse = new HashMap<>();
 
     for (String reportId : reports.split(",")) {
-      Map<String, Object> reportObject = reportList.get(Integer.parseInt(reportId.trim()));
+
+      Map<String, Object> reportObject =
+          reportList.stream()
+              .filter(r -> reportId.equals(r.get("id")))
+              .findFirst()
+              .orElseGet(() -> null);
+      if (reportObject == null) {
+        reportObject = reportList.get(Integer.parseInt(reportId.trim()));
+      }
       String sql = (String) reportObject.get("sql");
-      String name = (String) reportObject.get("name");
       List<Row> rows = schema.retrieveSql(sql, parameters);
       List<Object> result = new ArrayList<>();
       for (Row row : rows) {
@@ -51,7 +58,7 @@ public static void getJsonReport(Context ctx) throws JsonProcessingException {
         } else {
           result.add(row.getValueMap());
         }
-        jsonResponse.put(name, result);
+        jsonResponse.put(reportId, result);
       }
     }
     if (jsonResponse.size() == 1) {
diff --git a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
index dcac0857aa..4b293845d3 100644
--- a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
+++ b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
@@ -198,12 +198,11 @@ static void generateReportsToStore(
         throw new MolgenisException("Cannot find report id=" + reportId);
       }
       String sql = reportObject.get("sql");
-      String name = reportObject.get("name");
       List<Row> rows = schema.retrieveSql(sql, parameters);
       if (rows.size() > 0) {
-        store.writeTable(name, new ArrayList<>(rows.get(0).getColumnNames()), rows);
+        store.writeTable(reportId, new ArrayList<>(rows.get(0).getColumnNames()), rows);
       } else {
-        store.writeTable(name, new ArrayList<>(), rows);
+        store.writeTable(reportId, new ArrayList<>(), rows);
       }
     }
   }

From dd4c5ab0524083a7aac82a3375f43e3e252a9b3f Mon Sep 17 00:00:00 2001
From: mswertz <m.a.swertz@rug.nl>
Date: Wed, 27 Nov 2024 20:18:06 +0100
Subject: [PATCH 03/16] fix tests

---
 .../emx2/datamodels/PetStoreLoader.java       |  8 ++--
 .../emx2/graphql/TestGraphqlSchemaFields.java | 13 +++++-
 .../WebApiSmokeTests.java                     | 42 +++++++++++++++----
 3 files changed, 50 insertions(+), 13 deletions(-)

diff --git a/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/PetStoreLoader.java b/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/PetStoreLoader.java
index 3db119374d..56e7854f19 100644
--- a/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/PetStoreLoader.java
+++ b/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/PetStoreLoader.java
@@ -225,9 +225,9 @@ private void loadExampleData(Schema schema) {
         .getMetadata()
         .setSetting(
             "reports",
-            "[{\"id\":0,\"name\":\"pet report\",\"sql\":\"select * from \\\"Pet\\\"\"},"
-                + "{\"id\":1,\"name\":\"pet report with parameters\",\"sql\":\"select * from \\\"Pet\\\" p where p.name=ANY(${name:string_array})\"},"
-                + "{\"id\":2,\"name\":\"jsonb\",\"sql\":\"SELECT jsonb_agg(to_jsonb(\\\"Pet\\\")) AS result FROM \\\"Pet\\\"\"},"
-                + "{\"id\":3,\"name\":\"jsonb rows\",\"sql\":\"SELECT to_jsonb(\\\"Pet\\\") AS result FROM \\\"Pet\\\"\"}]");
+            "[{\"id\":\"report1\",\"name\":\"pet report\",\"sql\":\"select * from \\\"Pet\\\"\"},"
+                + "{\"id\":\"report2\",\"name\":\"pet report with parameters\",\"sql\":\"select * from \\\"Pet\\\" p where p.name=ANY(${name:string_array})\"},"
+                + "{\"id\":\"report3\",\"name\":\"jsonb\",\"sql\":\"SELECT jsonb_agg(to_jsonb(\\\"Pet\\\")) AS result FROM \\\"Pet\\\"\"},"
+                + "{\"id\":\"report4\",\"name\":\"jsonb rows\",\"sql\":\"SELECT to_jsonb(\\\"Pet\\\") AS result FROM \\\"Pet\\\"\"}]");
   }
 }
diff --git a/backend/molgenis-emx2-graphql/src/test/java/org/molgenis/emx2/graphql/TestGraphqlSchemaFields.java b/backend/molgenis-emx2-graphql/src/test/java/org/molgenis/emx2/graphql/TestGraphqlSchemaFields.java
index cb35c22fd7..24319d0c5f 100644
--- a/backend/molgenis-emx2-graphql/src/test/java/org/molgenis/emx2/graphql/TestGraphqlSchemaFields.java
+++ b/backend/molgenis-emx2-graphql/src/test/java/org/molgenis/emx2/graphql/TestGraphqlSchemaFields.java
@@ -833,12 +833,21 @@ public void testReport() throws IOException {
     schema = database.dropCreateSchema(schemaName);
     PET_STORE.getImportTask(schema, true).run();
     grapql = new GraphqlApiFactory().createGraphqlForSchema(schema, taskService);
-    JsonNode result = execute("{_reports(id:0){data,count}}");
+
+    // by index = 0
+    JsonNode result = execute("{_reports(id:\"0\"){data,count}}");
     assertTrue(result.at("/_reports/data").textValue().contains("pooky"));
     assertEquals(8, result.at("/_reports/count").intValue());
 
     // report 1 has parameters
-    result = execute("{_reports(id:1,parameters:{key:\"name\", value:\"spike\"}){data,count}}");
+    result = execute("{_reports(id:\"1\",parameters:{key:\"name\", value:\"spike\"}){data,count}}");
+    assertTrue(result.at("/_reports/data").textValue().contains("spike"));
+    assertEquals(1, result.at("/_reports/count").intValue());
+
+    // report by id=report1
+    result =
+        execute(
+            "{_reports(id:\"report2\",parameters:{key:\"name\", value:\"spike\"}){data,count}}");
     assertTrue(result.at("/_reports/data").textValue().contains("spike"));
     assertEquals(1, result.at("/_reports/count").intValue());
   }
diff --git a/backend/molgenis-emx2-webapi/src/test/java/org.molgenis.emx2.web/WebApiSmokeTests.java b/backend/molgenis-emx2-webapi/src/test/java/org.molgenis.emx2.web/WebApiSmokeTests.java
index 8f7f90524a..20f7918e15 100644
--- a/backend/molgenis-emx2-webapi/src/test/java/org.molgenis.emx2.web/WebApiSmokeTests.java
+++ b/backend/molgenis-emx2-webapi/src/test/java/org.molgenis.emx2.web/WebApiSmokeTests.java
@@ -174,6 +174,13 @@ public void testReports() throws IOException {
     TableStore store = new TableStoreForCsvInZipFile(zipFile.toPath());
     store.containsTable("pet report");
 
+    // check if 'id' also works
+    zipContents =
+        getContentAsByteArray(ACCEPT_ZIP, "/pet store reports/api/reports/zip?id=report1");
+    zipFile = createTempFile(zipContents, ".zip");
+    store = new TableStoreForCsvInZipFile(zipFile.toPath());
+    store.containsTable("pet report");
+
     // check if reports work with parameters
     zipContents =
         getContentAsByteArray(
@@ -187,29 +194,50 @@ public void testReports() throws IOException {
         getContentAsByteArray(ACCEPT_ZIP, "/pet store reports/api/reports/excel?id=0");
     File excelFile = createTempFile(excelContents, ".xlsx");
     store = new TableStoreForXlsxFile(excelFile.toPath());
-    assertTrue(store.containsTable("pet report"));
+    assertTrue(store.containsTable("0"));
+
+    // check if excel by id also works
+    excelContents =
+        getContentAsByteArray(ACCEPT_ZIP, "/pet store reports/api/reports/excel?id=report1");
+    excelFile = createTempFile(excelContents, ".xlsx");
+    store = new TableStoreForXlsxFile(excelFile.toPath());
+    assertTrue(store.containsTable("report1"));
 
     // check if reports work with parameters
     excelContents =
         getContentAsByteArray(
-            ACCEPT_ZIP, "/pet store reports/api/reports/excel?id=1&name=spike,pooky");
+            ACCEPT_ZIP, "/pet store reports/api/reports/excel?id=report2&name=spike,pooky");
     excelFile = createTempFile(excelContents, ".xlsx");
     store = new TableStoreForXlsxFile(excelFile.toPath());
-    assertTrue(store.containsTable("pet report with parameters"));
+    assertTrue(store.containsTable("report2"));
     assertTrue(excelContents.length > 0);
 
     // test json report api
     String jsonResults =
-        given().sessionId(SESSION_ID).get("/pet store reports/api/reports/json?id=0").asString();
-    assertFalse(jsonResults.contains("pet report"), "single result should not include report name");
+        given()
+            .sessionId(SESSION_ID)
+            .get("/pet store reports/api/reports/json?id=report1")
+            .asString();
+    assertFalse(
+        jsonResults.contains("report1"),
+        "single result should not include report name"); // are we sure about this?
     jsonResults =
         given()
             .sessionId(SESSION_ID)
-            .get("/pet store reports/api/reports/json?id=0,1&name=pooky")
+            .get("/pet store reports/api/reports/json?id=report1,report2&name=pooky")
             .asString();
     assertTrue(
-        jsonResults.contains("pet report"),
+        jsonResults.contains("report1"),
         "multiple results should use the report name to nest results");
+    // check that id is for keys
+    jsonResults =
+        given()
+            .sessionId(SESSION_ID)
+            .get("/pet store reports/api/reports/json?id=report1,report2&name=pooky")
+            .asString();
+    assertTrue(jsonResults.contains("report1"), "should use report id as key");
+    assertTrue(jsonResults.contains("report2"), "should use report id as key");
+
     jsonResults =
         given()
             .sessionId(SESSION_ID)

From 36ace8d9f796e6e9e034a0fb922b115d2c8729ba Mon Sep 17 00:00:00 2001
From: Ype Zijlstra <info@ypezijlstra.frl>
Date: Thu, 28 Nov 2024 11:16:59 +0100
Subject: [PATCH 04/16] typo fix

---
 apps/reports/src/components/ViewEditReport.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/apps/reports/src/components/ViewEditReport.vue b/apps/reports/src/components/ViewEditReport.vue
index 0342530b29..0a3b37f7b7 100644
--- a/apps/reports/src/components/ViewEditReport.vue
+++ b/apps/reports/src/components/ViewEditReport.vue
@@ -27,7 +27,7 @@
         id="reportName"
         v-model="name"
         label="name"
-        description="human readible label"
+        description="human readable label"
       />
       <InputText
         id="reportSql"

From c8b89acde90dd47d1ae181bf0800b9dffc049c7f Mon Sep 17 00:00:00 2001
From: Ype Zijlstra <info@ypezijlstra.frl>
Date: Thu, 28 Nov 2024 11:18:23 +0100
Subject: [PATCH 05/16] typo fix improvement

---
 apps/reports/src/components/ViewEditReport.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/apps/reports/src/components/ViewEditReport.vue b/apps/reports/src/components/ViewEditReport.vue
index 0a3b37f7b7..216c05f656 100644
--- a/apps/reports/src/components/ViewEditReport.vue
+++ b/apps/reports/src/components/ViewEditReport.vue
@@ -27,7 +27,7 @@
         id="reportName"
         v-model="name"
         label="name"
-        description="human readable label"
+        description="human-readable label"
       />
       <InputText
         id="reportSql"

From 60cefbdbf1ba8f271cf8f2b6f3be126519d6402c Mon Sep 17 00:00:00 2001
From: mswertz <m.a.swertz@rug.nl>
Date: Thu, 28 Nov 2024 12:17:03 +0100
Subject: [PATCH 06/16] process review comments

---
 apps/reports/src/components/ListReports.vue   |  6 ++--
 .../reports/src/components/ViewEditReport.vue | 25 +++++++--------
 .../emx2/datamodels/PetStoreLoader.java       |  8 ++---
 .../graphql/GraphqlSchemaFieldFactory.java    | 16 +++-------
 .../emx2/graphql/TestGraphqlSchemaFields.java | 10 +++---
 .../java/org/molgenis/emx2/web/JsonApi.java   | 31 ++++++++----------
 .../java/org/molgenis/emx2/web/ZipApi.java    | 16 ++--------
 .../WebApiSmokeTests.java                     | 32 +++++++------------
 8 files changed, 55 insertions(+), 89 deletions(-)

diff --git a/apps/reports/src/components/ListReports.vue b/apps/reports/src/components/ListReports.vue
index 586b666a2f..350f0cae02 100644
--- a/apps/reports/src/components/ListReports.vue
+++ b/apps/reports/src/components/ListReports.vue
@@ -32,7 +32,7 @@
       >
       <TableSimple
         @rowClick="open"
-        :columns="['index', 'id', 'name']"
+        :columns="['id', 'description']"
         :rows="reportsWithId"
         class="bg-white"
         selectColumn="id"
@@ -101,8 +101,6 @@ export default {
       if (this.reports) {
         let index = 0;
         return this.reports.map((report) => {
-          report.index = index++;
-          report.id = report.id || report.index;
           return report;
         });
       }
@@ -117,7 +115,7 @@ export default {
     },
     async add() {
       this.error = null;
-      this.reports.push({ id: "newid", name: "new report", sql: "" });
+      this.reports.push({ id: "uniqueid", description: "new report", sql: "" });
       await this.client
         .saveSetting("reports", this.reports)
         .catch((error) => (this.error = error));
diff --git a/apps/reports/src/components/ViewEditReport.vue b/apps/reports/src/components/ViewEditReport.vue
index 216c05f656..aae3104a9b 100644
--- a/apps/reports/src/components/ViewEditReport.vue
+++ b/apps/reports/src/components/ViewEditReport.vue
@@ -24,10 +24,10 @@
         description="unique index"
       />
       <InputString
-        id="reportName"
-        v-model="name"
-        label="name"
-        description="human-readable label"
+        id="reportDescription"
+        v-model="description"
+        label="description"
+        description="human-readable description"
       />
       <InputText
         id="reportSql"
@@ -42,9 +42,10 @@
       </div>
     </div>
     <h2 v-else>
-      Report: {{ name
-      }}<IconAction v-if="canEdit" icon="pencil-alt" @click="edit = true" />
+      Report: {{ id }}
+      <IconAction v-if="canEdit" icon="pencil-alt" @click="edit = true" />
     </h2>
+    <p>{{ description }}</p>
     <div v-if="parameterInputs">
       Please provide parameters:
       <FormInput
@@ -117,7 +118,7 @@ export default {
       count: null,
       id: null,
       sql: 'select * from "Pet"',
-      name: null,
+      label: null,
       parameters: {},
       error: null,
       success: null,
@@ -188,11 +189,7 @@ export default {
       const offset = this.limit * (this.page - 1);
       const result = await request(
         "graphql",
-        `query report($parameters:[MolgenisSettingsInput]) {_reports(id:"${
-          this.id || this.index
-        }",parameters:$parameters,limit:${
-          this.limit
-        },offset:${offset}){data,count}}`,
+        `query report($parameters:[MolgenisSettingsInput]) {_reports(id:${this.id},parameters:$parameters,limit:${this.limit},offset:${offset}){data,count}}`,
         {
           parameters: this.parameterKeyValueMap,
         }
@@ -216,7 +213,7 @@ export default {
       const reports = await this.client.fetchSettingValue("reports");
       reports[this.index].id = this.id;
       reports[this.index].sql = this.sql;
-      reports[this.index].name = this.name;
+      reports[this.index].label = this.label;
       this.client
         .saveSetting("reports", reports)
         .then((res) => {
@@ -230,7 +227,7 @@ export default {
       if (reports[this.index]) {
         this.id = reports[this.index].id;
         this.sql = reports[this.index].sql;
-        this.name = reports[this.index].name;
+        this.label = reports[this.index].label;
       } else {
         this.error = "report not found";
       }
diff --git a/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/PetStoreLoader.java b/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/PetStoreLoader.java
index 56e7854f19..1c64fb9a93 100644
--- a/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/PetStoreLoader.java
+++ b/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/PetStoreLoader.java
@@ -225,9 +225,9 @@ private void loadExampleData(Schema schema) {
         .getMetadata()
         .setSetting(
             "reports",
-            "[{\"id\":\"report1\",\"name\":\"pet report\",\"sql\":\"select * from \\\"Pet\\\"\"},"
-                + "{\"id\":\"report2\",\"name\":\"pet report with parameters\",\"sql\":\"select * from \\\"Pet\\\" p where p.name=ANY(${name:string_array})\"},"
-                + "{\"id\":\"report3\",\"name\":\"jsonb\",\"sql\":\"SELECT jsonb_agg(to_jsonb(\\\"Pet\\\")) AS result FROM \\\"Pet\\\"\"},"
-                + "{\"id\":\"report4\",\"name\":\"jsonb rows\",\"sql\":\"SELECT to_jsonb(\\\"Pet\\\") AS result FROM \\\"Pet\\\"\"}]");
+            "[{\"id\":\"report1\",\"label\":\"pet report\",\"sql\":\"select * from \\\"Pet\\\"\"},"
+                + "{\"id\":\"report2\",\"label\":\"pet report with parameters\",\"sql\":\"select * from \\\"Pet\\\" p where p.name=ANY(${name:string_array})\"},"
+                + "{\"id\":\"report3\",\"label\":\"jsonb\",\"sql\":\"SELECT jsonb_agg(to_jsonb(\\\"Pet\\\")) AS result FROM \\\"Pet\\\"\"},"
+                + "{\"id\":\"report4\",\"label\":\"jsonb rows\",\"sql\":\"SELECT to_jsonb(\\\"Pet\\\") AS result FROM \\\"Pet\\\"\"}]");
   }
 }
diff --git a/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java b/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java
index e041f89b21..7ec620177a 100644
--- a/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java
+++ b/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java
@@ -873,25 +873,19 @@ public GraphQLFieldDefinition schemaReportsField(Schema schema) {
               try {
                 String reportsJson = schema.getMetadata().getSetting("reports");
                 logger.info("REPORT value: " + reportsJson);
+                final String id = dataFetchingEnvironment.getArgument(ID);
                 if (reportsJson != null) {
-                  final String id = dataFetchingEnvironment.getArgument(ID);
                   Integer offset = dataFetchingEnvironment.getArgumentOrDefault(OFFSET, 0);
                   Integer limit = dataFetchingEnvironment.getArgumentOrDefault(LIMIT, 10);
                   Map<String, String> parameters =
                       convertKeyValueListToMap(dataFetchingEnvironment.getArgument(PARAMETERS));
                   List<Map<String, Object>> reportList =
                       new ObjectMapper().readValue(reportsJson, List.class);
-                  Map<String, Object> report =
-                      reportList.stream()
-                          .filter(r -> id.equals(r.get("id")))
-                          .findFirst()
-                          .orElseGet(() -> null);
-                  if (report == null) {
-                    report = reportList.get(Integer.parseInt(id));
-                  }
-                  String sql = report.get("sql") + " LIMIT " + limit + " OFFSET " + offset;
+                  Optional<Map<String, Object>> report =
+                      reportList.stream().filter(r -> id.equals(r.get("id"))).findFirst();
+                  String sql = report.get().get("sql") + " LIMIT " + limit + " OFFSET " + offset;
                   String countSql =
-                      String.format("select count(*) from (%s) as count", report.get("sql"));
+                      String.format("select count(*) from (%s) as count", report.get().get("sql"));
                   result.put(DATA, convertToJson(schema.retrieveSql(sql, parameters)));
                   result.put(
                       COUNT,
diff --git a/backend/molgenis-emx2-graphql/src/test/java/org/molgenis/emx2/graphql/TestGraphqlSchemaFields.java b/backend/molgenis-emx2-graphql/src/test/java/org/molgenis/emx2/graphql/TestGraphqlSchemaFields.java
index 23f8709b9b..2468d76e61 100644
--- a/backend/molgenis-emx2-graphql/src/test/java/org/molgenis/emx2/graphql/TestGraphqlSchemaFields.java
+++ b/backend/molgenis-emx2-graphql/src/test/java/org/molgenis/emx2/graphql/TestGraphqlSchemaFields.java
@@ -875,14 +875,14 @@ public void testReport() throws IOException {
     schema = database.dropCreateSchema(schemaName);
     PET_STORE.getImportTask(schema, true).run();
     grapql = new GraphqlApiFactory().createGraphqlForSchema(schema, taskService);
-
-    // by index = 0
-    JsonNode result = execute("{_reports(id:\"0\"){data,count}}");
+    JsonNode result = execute("{_reports(id:\"report1\"){data,count}}");
     assertTrue(result.at("/_reports/data").textValue().contains("pooky"));
     assertEquals(8, result.at("/_reports/count").intValue());
 
-    // report 1 has parameters
-    result = execute("{_reports(id:\"1\",parameters:{key:\"name\", value:\"spike\"}){data,count}}");
+    // report 2 has parameters
+    result =
+        execute(
+            "{_reports(id:\"report2\",parameters:{key:\"name\", value:\"spike\"}){data,count}}");
     assertTrue(result.at("/_reports/data").textValue().contains("spike"));
     assertEquals(1, result.at("/_reports/count").intValue());
 
diff --git a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/JsonApi.java b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/JsonApi.java
index 3e0bc3efff..f413f159b6 100644
--- a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/JsonApi.java
+++ b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/JsonApi.java
@@ -7,11 +7,9 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import io.javalin.Javalin;
 import io.javalin.http.Context;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 import org.jooq.JSONB;
+import org.molgenis.emx2.MolgenisException;
 import org.molgenis.emx2.Row;
 import org.molgenis.emx2.Schema;
 
@@ -31,22 +29,12 @@ public static void getJsonReport(Context ctx) throws JsonProcessingException {
     String reports = ctx.queryParam("id");
     Map<String, Object> parameters = getReportParameters(ctx);
     String reportsJson = schema.getMetadata().getSetting("reports");
-
     ObjectMapper mapper = new ObjectMapper();
-    List<Map<String, Object>> reportList = mapper.readValue(reportsJson, List.class);
+    List<Map<String, String>> reportList = mapper.readValue(reportsJson, List.class);
     Map<String, Object> jsonResponse = new HashMap<>();
-
     for (String reportId : reports.split(",")) {
-
-      Map<String, Object> reportObject =
-          reportList.stream()
-              .filter(r -> reportId.equals(r.get("id")))
-              .findFirst()
-              .orElseGet(() -> null);
-      if (reportObject == null) {
-        reportObject = reportList.get(Integer.parseInt(reportId.trim()));
-      }
-      String sql = (String) reportObject.get("sql");
+      Map<String, String> reportObject = getReportById(reportId, reportList);
+      String sql = reportObject.get("sql");
       List<Row> rows = schema.retrieveSql(sql, parameters);
       List<Object> result = new ArrayList<>();
       for (Row row : rows) {
@@ -67,4 +55,13 @@ public static void getJsonReport(Context ctx) throws JsonProcessingException {
       ctx.json(jsonResponse);
     }
   }
+
+  static Map<String, String> getReportById(String reportId, List<Map<String, String>> reportList) {
+    Optional<Map<String, String>> reportOptional =
+        reportList.stream().filter(r -> reportId.equals(r.get("id"))).findFirst();
+    if (!reportOptional.isPresent()) {
+      throw new MolgenisException("Report not found id=" + reportId);
+    }
+    return reportOptional.get();
+  }
 }
diff --git a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
index 4b293845d3..f01b2a1c86 100644
--- a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
+++ b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
@@ -2,6 +2,7 @@
 
 import static org.molgenis.emx2.web.Constants.TABLE;
 import static org.molgenis.emx2.web.DownloadApiUtils.includeSystemColumns;
+import static org.molgenis.emx2.web.JsonApi.getReportById;
 import static org.molgenis.emx2.web.MolgenisWebservice.getSchema;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
@@ -183,20 +184,7 @@ static void generateReportsToStore(
     String reportsJson = schema.getMetadata().getSetting("reports");
     List<Map<String, String>> reportList = new ObjectMapper().readValue(reportsJson, List.class);
     for (String reportId : reports.split(",")) {
-      // first find report object based on id
-      Optional<Map<String, String>> found =
-          reportList.stream()
-              .filter(reportDefinition -> reportId.equals(reportDefinition.get("id")))
-              .findFirst();
-      Map<String, String> reportObject = null;
-      if (found.isPresent()) {
-        reportObject = found.get();
-      } else {
-        reportObject = reportList.get(Integer.parseInt(reportId));
-      }
-      if (reportObject == null) {
-        throw new MolgenisException("Cannot find report id=" + reportId);
-      }
+      Map<String, String> reportObject = getReportById(reportId, reportList);
       String sql = reportObject.get("sql");
       List<Row> rows = schema.retrieveSql(sql, parameters);
       if (rows.size() > 0) {
diff --git a/backend/molgenis-emx2-webapi/src/test/java/org.molgenis.emx2.web/WebApiSmokeTests.java b/backend/molgenis-emx2-webapi/src/test/java/org.molgenis.emx2.web/WebApiSmokeTests.java
index aa92f4c9ac..f21c2529f2 100644
--- a/backend/molgenis-emx2-webapi/src/test/java/org.molgenis.emx2.web/WebApiSmokeTests.java
+++ b/backend/molgenis-emx2-webapi/src/test/java/org.molgenis.emx2.web/WebApiSmokeTests.java
@@ -169,37 +169,23 @@ public void testReports() throws IOException {
 
     // check if reports work
     byte[] zipContents =
-        getContentAsByteArray(ACCEPT_ZIP, "/pet store reports/api/reports/zip?id=0");
+        getContentAsByteArray(ACCEPT_ZIP, "/pet store reports/api/reports/zip?id=report1");
     File zipFile = createTempFile(zipContents, ".zip");
     TableStore store = new TableStoreForCsvInZipFile(zipFile.toPath());
     store.containsTable("pet report");
 
-    // check if 'id' also works
-    zipContents =
-        getContentAsByteArray(ACCEPT_ZIP, "/pet store reports/api/reports/zip?id=report1");
-    zipFile = createTempFile(zipContents, ".zip");
-    store = new TableStoreForCsvInZipFile(zipFile.toPath());
-    store.containsTable("pet report");
-
     // check if reports work with parameters
     zipContents =
         getContentAsByteArray(
-            ACCEPT_ZIP, "/pet store reports/api/reports/zip?id=1&name=spike,pooky");
+            ACCEPT_ZIP, "/pet store reports/api/reports/zip?id=report2&name=spike,pooky");
     zipFile = createTempFile(zipContents, ".zip");
     store = new TableStoreForCsvInZipFile(zipFile.toPath());
     store.containsTable("pet report with parameters");
 
     // check if reports work
     byte[] excelContents =
-        getContentAsByteArray(ACCEPT_ZIP, "/pet store reports/api/reports/excel?id=0");
-    File excelFile = createTempFile(excelContents, ".xlsx");
-    store = new TableStoreForXlsxFile(excelFile.toPath());
-    assertTrue(store.containsTable("0"));
-
-    // check if excel by id also works
-    excelContents =
         getContentAsByteArray(ACCEPT_ZIP, "/pet store reports/api/reports/excel?id=report1");
-    excelFile = createTempFile(excelContents, ".xlsx");
+    File excelFile = createTempFile(excelContents, ".xlsx");
     store = new TableStoreForXlsxFile(excelFile.toPath());
     assertTrue(store.containsTable("report1"));
 
@@ -241,20 +227,26 @@ public void testReports() throws IOException {
     jsonResults =
         given()
             .sessionId(SESSION_ID)
-            .get("/pet store reports/api/reports/json?id=1&name=spike,pooky")
+            .get("/pet store reports/api/reports/json?id=report2&name=spike,pooky")
             .asString();
     assertTrue(jsonResults.contains("pooky"));
 
     // test report using jsonb_agg
     jsonResults =
-        given().sessionId(SESSION_ID).get("/pet store reports/api/reports/json?id=2").asString();
+        given()
+            .sessionId(SESSION_ID)
+            .get("/pet store reports/api/reports/json?id=report3")
+            .asString();
     ObjectMapper objectMapper = new ObjectMapper();
     List<Object> jsonbResult = objectMapper.readValue(jsonResults, List.class);
     assertTrue(jsonbResult.get(0).toString().contains("pooky"));
 
     // test report using jsonb rows
     jsonResults =
-        given().sessionId(SESSION_ID).get("/pet store reports/api/reports/json?id=3").asString();
+        given()
+            .sessionId(SESSION_ID)
+            .get("/pet store reports/api/reports/json?id=report4")
+            .asString();
     jsonbResult = objectMapper.readValue(jsonResults, List.class);
     assertTrue(jsonbResult.get(0).toString().contains("pooky"));
   }

From 53751c8b4d6d6c466aef0234823e8f285b8c85c4 Mon Sep 17 00:00:00 2001
From: mswertz <m.a.swertz@rug.nl>
Date: Thu, 28 Nov 2024 12:29:41 +0100
Subject: [PATCH 07/16] process review comments

---
 apps/reports/src/components/ListReports.vue   |  1 +
 .../reports/src/components/ViewEditReport.vue |  2 +-
 .../emx2/datamodels/PetStoreLoader.java       |  8 +++---
 docs/molgenis/use_reports.md                  | 26 ++++++++++++++++---
 4 files changed, 29 insertions(+), 8 deletions(-)

diff --git a/apps/reports/src/components/ListReports.vue b/apps/reports/src/components/ListReports.vue
index 350f0cae02..9e574ed32c 100644
--- a/apps/reports/src/components/ListReports.vue
+++ b/apps/reports/src/components/ListReports.vue
@@ -101,6 +101,7 @@ export default {
       if (this.reports) {
         let index = 0;
         return this.reports.map((report) => {
+          report.index = index++;
           return report;
         });
       }
diff --git a/apps/reports/src/components/ViewEditReport.vue b/apps/reports/src/components/ViewEditReport.vue
index aae3104a9b..e8eba50c60 100644
--- a/apps/reports/src/components/ViewEditReport.vue
+++ b/apps/reports/src/components/ViewEditReport.vue
@@ -189,7 +189,7 @@ export default {
       const offset = this.limit * (this.page - 1);
       const result = await request(
         "graphql",
-        `query report($parameters:[MolgenisSettingsInput]) {_reports(id:${this.id},parameters:$parameters,limit:${this.limit},offset:${offset}){data,count}}`,
+        `query report($parameters:[MolgenisSettingsInput]) {_reports(id:"${this.id}",parameters:$parameters,limit:${this.limit},offset:${offset}){data,count}}`,
         {
           parameters: this.parameterKeyValueMap,
         }
diff --git a/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/PetStoreLoader.java b/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/PetStoreLoader.java
index 1c64fb9a93..177496a940 100644
--- a/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/PetStoreLoader.java
+++ b/backend/molgenis-emx2-datamodels/src/main/java/org/molgenis/emx2/datamodels/PetStoreLoader.java
@@ -225,9 +225,9 @@ private void loadExampleData(Schema schema) {
         .getMetadata()
         .setSetting(
             "reports",
-            "[{\"id\":\"report1\",\"label\":\"pet report\",\"sql\":\"select * from \\\"Pet\\\"\"},"
-                + "{\"id\":\"report2\",\"label\":\"pet report with parameters\",\"sql\":\"select * from \\\"Pet\\\" p where p.name=ANY(${name:string_array})\"},"
-                + "{\"id\":\"report3\",\"label\":\"jsonb\",\"sql\":\"SELECT jsonb_agg(to_jsonb(\\\"Pet\\\")) AS result FROM \\\"Pet\\\"\"},"
-                + "{\"id\":\"report4\",\"label\":\"jsonb rows\",\"sql\":\"SELECT to_jsonb(\\\"Pet\\\") AS result FROM \\\"Pet\\\"\"}]");
+            "[{\"id\":\"report1\",\"description\":\"pet report\",\"sql\":\"select * from \\\"Pet\\\"\"},"
+                + "{\"id\":\"report2\",\"description\":\"pet report with parameters\",\"sql\":\"select * from \\\"Pet\\\" p where p.name=ANY(${name:string_array})\"},"
+                + "{\"id\":\"report3\",\"description\":\"jsonb\",\"sql\":\"SELECT jsonb_agg(to_jsonb(\\\"Pet\\\")) AS result FROM \\\"Pet\\\"\"},"
+                + "{\"id\":\"report4\",\"description\":\"jsonb rows\",\"sql\":\"SELECT to_jsonb(\\\"Pet\\\") AS result FROM \\\"Pet\\\"\"}]");
   }
 }
diff --git a/docs/molgenis/use_reports.md b/docs/molgenis/use_reports.md
index dbcfe9cc76..e6d96c3322 100644
--- a/docs/molgenis/use_reports.md
+++ b/docs/molgenis/use_reports.md
@@ -19,6 +19,26 @@ Example of a report:
 
 ```select * from "Pet"```
 
+Each report requires an unique id to retrieve, and an optional human readable description.
+
+n.b. since version 12 the 'id' is required and used, please update reports when you created them before 12. Technically reports are stored as json into 
+settings under key 'reports', for example: 
+
+```
+[
+   {
+      "id":"report1",
+      "label":"pet report",
+      "sql":"select * from \"Pet\""
+   },
+   {
+      "id":"report2",
+      "label":"pet report with parameters",
+      "sql":"select * from \"Pet\" p where p.name=ANY(${name:string_array})"
+   },
+]
+```
+
 # Using parameters
 
 You can parameterize your queries using ```${name}``` or when you need strong typing ```${name:string_array}```
@@ -36,9 +56,9 @@ it into SQL.
 
 You can also use these reports in scripts, to directly download the results, for example:
 
-* http://myserver.com/schema/api/report/1
-* http://myserver.com/schema/api/report/1,2 (then you get result from two reports)
-* http://myserver.com/schema/api/report/1,2?name=pooky,spike (then you get result from two reports using 'name' as parameter)
+* http://myserver.com/schema/api/report/report1
+* http://myserver.com/schema/api/report/report1,report2 (then you get result from two reports)
+* http://myserver.com/schema/api/report/report2,report3?name=pooky,spike (then you get result from two reports using 'name' as parameter)
 
 # Returning JSON so you can use reports as REST like 'get' API
 

From 315b06f7b33bed5bfb450a2bd7226acdbe0ae760 Mon Sep 17 00:00:00 2001
From: mswertz <m.a.swertz@rug.nl>
Date: Thu, 28 Nov 2024 12:32:06 +0100
Subject: [PATCH 08/16] layout fixes

---
 apps/reports/src/components/ViewEditReport.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/apps/reports/src/components/ViewEditReport.vue b/apps/reports/src/components/ViewEditReport.vue
index e8eba50c60..cccefd5e1f 100644
--- a/apps/reports/src/components/ViewEditReport.vue
+++ b/apps/reports/src/components/ViewEditReport.vue
@@ -42,10 +42,10 @@
       </div>
     </div>
     <h2 v-else>
-      Report: {{ id }}
+      View report id={{ id }}
       <IconAction v-if="canEdit" icon="pencil-alt" @click="edit = true" />
     </h2>
-    <p>{{ description }}</p>
+    <p v-if="description">Description: {{ description }}</p>
     <div v-if="parameterInputs">
       Please provide parameters:
       <FormInput

From 6e6db804ba7fdb8215d7ad3b5f62f2c9332315a3 Mon Sep 17 00:00:00 2001
From: mswertz <m.a.swertz@rug.nl>
Date: Thu, 28 Nov 2024 12:33:07 +0100
Subject: [PATCH 09/16] remove annotation

---
 .../src/main/java/org/molgenis/emx2/web/ZipApi.java           | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
index f01b2a1c86..b444de643a 100644
--- a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
+++ b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
@@ -175,9 +175,7 @@ static void getZippedReports(Context ctx) throws IOException {
     }
   }
 
-  static void generateReportsToStore(
-      @org.jetbrains.annotations.NotNull Context ctx, TableStore store)
-      throws JsonProcessingException {
+  static void generateReportsToStore(Context ctx, TableStore store) throws JsonProcessingException {
     String reports = ctx.queryParam("id");
     Schema schema = getSchema(ctx);
     Map<String, ?> parameters = getReportParameters(ctx);

From ba330e5371816e713f22bc931ad601596128bdbf Mon Sep 17 00:00:00 2001
From: mswertz <m.a.swertz@rug.nl>
Date: Thu, 28 Nov 2024 12:46:53 +0100
Subject: [PATCH 10/16] fix rename to description

---
 apps/reports/src/components/ViewEditReport.vue | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/apps/reports/src/components/ViewEditReport.vue b/apps/reports/src/components/ViewEditReport.vue
index cccefd5e1f..f91fef8dbf 100644
--- a/apps/reports/src/components/ViewEditReport.vue
+++ b/apps/reports/src/components/ViewEditReport.vue
@@ -118,7 +118,7 @@ export default {
       count: null,
       id: null,
       sql: 'select * from "Pet"',
-      label: null,
+      description: null,
       parameters: {},
       error: null,
       success: null,
@@ -213,7 +213,7 @@ export default {
       const reports = await this.client.fetchSettingValue("reports");
       reports[this.index].id = this.id;
       reports[this.index].sql = this.sql;
-      reports[this.index].label = this.label;
+      reports[this.index].description = this.description;
       this.client
         .saveSetting("reports", reports)
         .then((res) => {
@@ -227,7 +227,7 @@ export default {
       if (reports[this.index]) {
         this.id = reports[this.index].id;
         this.sql = reports[this.index].sql;
-        this.label = reports[this.index].label;
+        this.description = reports[this.index].description;
       } else {
         this.error = "report not found";
       }

From ddcefc3b7165b43f87b0a4878959881c2b382354 Mon Sep 17 00:00:00 2001
From: mswertz <m.a.swertz@rug.nl>
Date: Thu, 28 Nov 2024 18:09:54 +0100
Subject: [PATCH 11/16] shorten code further

---
 .../graphql/GraphqlSchemaFieldFactory.java    | 50 ++++++++++++-------
 .../java/org/molgenis/emx2/web/JsonApi.java   | 18 ++-----
 .../java/org/molgenis/emx2/web/ZipApi.java    |  7 ++-
 3 files changed, 37 insertions(+), 38 deletions(-)

diff --git a/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java b/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java
index 7ec620177a..9cd2b9f157 100644
--- a/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java
+++ b/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java
@@ -871,26 +871,20 @@ public GraphQLFieldDefinition schemaReportsField(Schema schema) {
             dataFetchingEnvironment -> {
               Map<String, Object> result = new LinkedHashMap<>();
               try {
-                String reportsJson = schema.getMetadata().getSetting("reports");
-                logger.info("REPORT value: " + reportsJson);
                 final String id = dataFetchingEnvironment.getArgument(ID);
-                if (reportsJson != null) {
-                  Integer offset = dataFetchingEnvironment.getArgumentOrDefault(OFFSET, 0);
-                  Integer limit = dataFetchingEnvironment.getArgumentOrDefault(LIMIT, 10);
-                  Map<String, String> parameters =
-                      convertKeyValueListToMap(dataFetchingEnvironment.getArgument(PARAMETERS));
-                  List<Map<String, Object>> reportList =
-                      new ObjectMapper().readValue(reportsJson, List.class);
-                  Optional<Map<String, Object>> report =
-                      reportList.stream().filter(r -> id.equals(r.get("id"))).findFirst();
-                  String sql = report.get().get("sql") + " LIMIT " + limit + " OFFSET " + offset;
-                  String countSql =
-                      String.format("select count(*) from (%s) as count", report.get().get("sql"));
-                  result.put(DATA, convertToJson(schema.retrieveSql(sql, parameters)));
-                  result.put(
-                      COUNT,
-                      schema.retrieveSql(countSql, parameters).get(0).get("count", Integer.class));
-                }
+
+                Integer offset = dataFetchingEnvironment.getArgumentOrDefault(OFFSET, 0);
+                Integer limit = dataFetchingEnvironment.getArgumentOrDefault(LIMIT, 10);
+                Map<String, String> parameters =
+                    convertKeyValueListToMap(dataFetchingEnvironment.getArgument(PARAMETERS));
+                Map<String, String> report = getReportById(id, schema);
+                String sql = report.get("sql") + " LIMIT " + limit + " OFFSET " + offset;
+                String countSql =
+                    String.format("select count(*) from (%s) as count", report.get("sql"));
+                result.put(DATA, convertToJson(schema.retrieveSql(sql, parameters)));
+                result.put(
+                    COUNT,
+                    schema.retrieveSql(countSql, parameters).get(0).get("count", Integer.class));
                 return result;
               } catch (Exception e) {
                 throw new MolgenisException(
@@ -901,6 +895,24 @@ public GraphQLFieldDefinition schemaReportsField(Schema schema) {
         .build();
   }
 
+  public static Map<String, String> getReportById(String reportId, Schema schema) {
+    try {
+      String reportsJson = schema.getMetadata().getSetting("reports");
+      List<Map<String, String>> reportList = new ObjectMapper().readValue(reportsJson, List.class);
+      if (reportsJson != null) {
+        Optional<Map<String, String>> reportOptional =
+            reportList.stream().filter(r -> reportId.equals(r.get("id"))).findFirst();
+        if (reportOptional.isPresent()) {
+
+          return reportOptional.get();
+        }
+      }
+    } catch (Exception e) {
+      // nothing to do, error will be handled below
+    }
+    throw new MolgenisException("Report not found id=" + reportId);
+  }
+
   private String convertToJson(List<Row> rows) {
     ObjectMapper objectMapper = new ObjectMapper();
     try {
diff --git a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/JsonApi.java b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/JsonApi.java
index f413f159b6..3391b4d9e5 100644
--- a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/JsonApi.java
+++ b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/JsonApi.java
@@ -1,5 +1,6 @@
 package org.molgenis.emx2.web;
 
+import static org.molgenis.emx2.graphql.GraphqlSchemaFieldFactory.getReportById;
 import static org.molgenis.emx2.web.MolgenisWebservice.getSchema;
 import static org.molgenis.emx2.web.ZipApi.getReportParameters;
 
@@ -9,7 +10,6 @@
 import io.javalin.http.Context;
 import java.util.*;
 import org.jooq.JSONB;
-import org.molgenis.emx2.MolgenisException;
 import org.molgenis.emx2.Row;
 import org.molgenis.emx2.Schema;
 
@@ -28,14 +28,11 @@ public static void getJsonReport(Context ctx) throws JsonProcessingException {
     Schema schema = getSchema(ctx);
     String reports = ctx.queryParam("id");
     Map<String, Object> parameters = getReportParameters(ctx);
-    String reportsJson = schema.getMetadata().getSetting("reports");
     ObjectMapper mapper = new ObjectMapper();
-    List<Map<String, String>> reportList = mapper.readValue(reportsJson, List.class);
     Map<String, Object> jsonResponse = new HashMap<>();
     for (String reportId : reports.split(",")) {
-      Map<String, String> reportObject = getReportById(reportId, reportList);
-      String sql = reportObject.get("sql");
-      List<Row> rows = schema.retrieveSql(sql, parameters);
+      Map<String, String> report = getReportById(reportId, schema);
+      List<Row> rows = schema.retrieveSql(report.get("sql"), parameters);
       List<Object> result = new ArrayList<>();
       for (Row row : rows) {
         // single json object will not be nested in key/value
@@ -55,13 +52,4 @@ public static void getJsonReport(Context ctx) throws JsonProcessingException {
       ctx.json(jsonResponse);
     }
   }
-
-  static Map<String, String> getReportById(String reportId, List<Map<String, String>> reportList) {
-    Optional<Map<String, String>> reportOptional =
-        reportList.stream().filter(r -> reportId.equals(r.get("id"))).findFirst();
-    if (!reportOptional.isPresent()) {
-      throw new MolgenisException("Report not found id=" + reportId);
-    }
-    return reportOptional.get();
-  }
 }
diff --git a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
index b444de643a..8851da3534 100644
--- a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
+++ b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
@@ -1,8 +1,8 @@
 package org.molgenis.emx2.web;
 
+import static org.molgenis.emx2.graphql.GraphqlSchemaFieldFactory.getReportById;
 import static org.molgenis.emx2.web.Constants.TABLE;
 import static org.molgenis.emx2.web.DownloadApiUtils.includeSystemColumns;
-import static org.molgenis.emx2.web.JsonApi.getReportById;
 import static org.molgenis.emx2.web.MolgenisWebservice.getSchema;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
@@ -182,9 +182,8 @@ static void generateReportsToStore(Context ctx, TableStore store) throws JsonPro
     String reportsJson = schema.getMetadata().getSetting("reports");
     List<Map<String, String>> reportList = new ObjectMapper().readValue(reportsJson, List.class);
     for (String reportId : reports.split(",")) {
-      Map<String, String> reportObject = getReportById(reportId, reportList);
-      String sql = reportObject.get("sql");
-      List<Row> rows = schema.retrieveSql(sql, parameters);
+      Map<String, String> report = getReportById(reportId, schema);
+      List<Row> rows = schema.retrieveSql(report.get("sql"), parameters);
       if (rows.size() > 0) {
         store.writeTable(reportId, new ArrayList<>(rows.get(0).getColumnNames()), rows);
       } else {

From 09dd1668d476fd7de8ee9e1c7097f924648605ba Mon Sep 17 00:00:00 2001
From: mswertz <m.a.swertz@rug.nl>
Date: Thu, 28 Nov 2024 18:43:52 +0100
Subject: [PATCH 12/16] refactor code

---
 .../graphql/GraphqlSchemaFieldFactory.java    | 51 +------------
 .../molgenis/emx2/settings/ReportUtils.java   | 73 +++++++++++++++++++
 .../java/org/molgenis/emx2/web/JsonApi.java   | 21 +-----
 .../java/org/molgenis/emx2/web/ZipApi.java    | 11 +--
 .../WebApiSmokeTests.java                     |  4 +-
 5 files changed, 85 insertions(+), 75 deletions(-)
 create mode 100644 backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/settings/ReportUtils.java

diff --git a/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java b/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java
index 9cd2b9f157..fdcf0da383 100644
--- a/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java
+++ b/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java
@@ -8,6 +8,8 @@
 import static org.molgenis.emx2.graphql.GraphqlConstants.INHERITED;
 import static org.molgenis.emx2.graphql.GraphqlConstants.KEY;
 import static org.molgenis.emx2.json.JsonUtil.jsonToSchema;
+import static org.molgenis.emx2.settings.ReportUtils.getReportAsJson;
+import static org.molgenis.emx2.settings.ReportUtils.getReportCount;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import graphql.Scalars;
@@ -15,7 +17,6 @@
 import java.io.IOException;
 import java.util.*;
 import java.util.stream.Stream;
-import org.jooq.JSONB;
 import org.molgenis.emx2.*;
 import org.molgenis.emx2.json.JsonUtil;
 import org.molgenis.emx2.sql.SqlDatabase;
@@ -872,19 +873,12 @@ public GraphQLFieldDefinition schemaReportsField(Schema schema) {
               Map<String, Object> result = new LinkedHashMap<>();
               try {
                 final String id = dataFetchingEnvironment.getArgument(ID);
-
                 Integer offset = dataFetchingEnvironment.getArgumentOrDefault(OFFSET, 0);
                 Integer limit = dataFetchingEnvironment.getArgumentOrDefault(LIMIT, 10);
                 Map<String, String> parameters =
                     convertKeyValueListToMap(dataFetchingEnvironment.getArgument(PARAMETERS));
-                Map<String, String> report = getReportById(id, schema);
-                String sql = report.get("sql") + " LIMIT " + limit + " OFFSET " + offset;
-                String countSql =
-                    String.format("select count(*) from (%s) as count", report.get("sql"));
-                result.put(DATA, convertToJson(schema.retrieveSql(sql, parameters)));
-                result.put(
-                    COUNT,
-                    schema.retrieveSql(countSql, parameters).get(0).get("count", Integer.class));
+                result.put(DATA, getReportAsJson(id, schema, parameters, limit, offset));
+                result.put(COUNT, getReportCount(id, schema, parameters));
                 return result;
               } catch (Exception e) {
                 throw new MolgenisException(
@@ -894,41 +888,4 @@ public GraphQLFieldDefinition schemaReportsField(Schema schema) {
             })
         .build();
   }
-
-  public static Map<String, String> getReportById(String reportId, Schema schema) {
-    try {
-      String reportsJson = schema.getMetadata().getSetting("reports");
-      List<Map<String, String>> reportList = new ObjectMapper().readValue(reportsJson, List.class);
-      if (reportsJson != null) {
-        Optional<Map<String, String>> reportOptional =
-            reportList.stream().filter(r -> reportId.equals(r.get("id"))).findFirst();
-        if (reportOptional.isPresent()) {
-
-          return reportOptional.get();
-        }
-      }
-    } catch (Exception e) {
-      // nothing to do, error will be handled below
-    }
-    throw new MolgenisException("Report not found id=" + reportId);
-  }
-
-  private String convertToJson(List<Row> rows) {
-    ObjectMapper objectMapper = new ObjectMapper();
-    try {
-      List<Map<String, Object>> result = new ArrayList<>();
-      for (Row row : rows) {
-        if (row.getValueMap().size() == 1) {
-          Object value = row.getValueMap().values().iterator().next();
-          if (value instanceof JSONB) {
-            return value.toString();
-          }
-        }
-        result.add(row.getValueMap());
-      }
-      return objectMapper.writeValueAsString(result);
-    } catch (Exception e) {
-      throw new MolgenisException("Cannot convert sql result set to json", e);
-    }
-  }
 }
diff --git a/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/settings/ReportUtils.java b/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/settings/ReportUtils.java
new file mode 100644
index 0000000000..f03f072d81
--- /dev/null
+++ b/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/settings/ReportUtils.java
@@ -0,0 +1,73 @@
+package org.molgenis.emx2.settings;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+import org.jooq.JSONB;
+import org.molgenis.emx2.MolgenisException;
+import org.molgenis.emx2.Row;
+import org.molgenis.emx2.Schema;
+
+public class ReportUtils {
+  public static Map<String, String> getReportById(String reportId, Schema schema) {
+    try {
+      String reportsJson = schema.getMetadata().getSetting("reports");
+      List<Map<String, String>> reportList = new ObjectMapper().readValue(reportsJson, List.class);
+      if (reportsJson != null) {
+        Optional<Map<String, String>> reportOptional =
+            reportList.stream().filter(r -> reportId.equals(r.get("id"))).findFirst();
+        if (reportOptional.isPresent()) {
+
+          return reportOptional.get();
+        }
+      }
+    } catch (Exception e) {
+      // nothing to do, error will be handled below
+    }
+    throw new MolgenisException("Report not found id=" + reportId);
+  }
+
+  public static String getReportAsJson(String id, Schema schema, Map<String, ?> parameters) {
+    Map<String, String> report = getReportById(id, schema);
+    return convertToJson(schema.retrieveSql(report.get("sql"), parameters));
+  }
+
+  public static String getReportAsJson(
+      String id, Schema schema, Map<String, ?> parameters, int limit, int offset) {
+    Map<String, String> report = getReportById(id, schema);
+    String sql = report.get("sql") + " LIMIT " + limit + " OFFSET " + offset;
+    return convertToJson(schema.retrieveSql(sql, parameters));
+  }
+
+  public static List<Row> getReportAsRows(String id, Schema schema, Map<String, ?> parameters) {
+    Map<String, String> report = getReportById(id, schema);
+    return schema.retrieveSql(report.get("sql"), parameters);
+  }
+
+  public static Integer getReportCount(String id, Schema schema, Map<String, ?> parameters) {
+    Map<String, String> report = getReportById(id, schema);
+    String countSql = String.format("select count(*) from (%s) as count", report.get("sql"));
+    return schema.retrieveSql(countSql, parameters).get(0).get("count", Integer.class);
+  }
+
+  private static String convertToJson(List<Row> rows) {
+    ObjectMapper objectMapper = new ObjectMapper();
+    try {
+      List<Map<String, Object>> result = new ArrayList<>();
+      for (Row row : rows) {
+        if (row.getValueMap().size() == 1) {
+          Object value = row.getValueMap().values().iterator().next();
+          if (value instanceof JSONB) {
+            return value.toString();
+          }
+        }
+        result.add(row.getValueMap());
+      }
+      return objectMapper.writeValueAsString(result);
+    } catch (Exception e) {
+      throw new MolgenisException("Cannot convert sql result set to json", e);
+    }
+  }
+}
diff --git a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/JsonApi.java b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/JsonApi.java
index 3391b4d9e5..cbaad1d955 100644
--- a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/JsonApi.java
+++ b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/JsonApi.java
@@ -1,6 +1,6 @@
 package org.molgenis.emx2.web;
 
-import static org.molgenis.emx2.graphql.GraphqlSchemaFieldFactory.getReportById;
+import static org.molgenis.emx2.settings.ReportUtils.getReportAsJson;
 import static org.molgenis.emx2.web.MolgenisWebservice.getSchema;
 import static org.molgenis.emx2.web.ZipApi.getReportParameters;
 
@@ -9,8 +9,6 @@
 import io.javalin.Javalin;
 import io.javalin.http.Context;
 import java.util.*;
-import org.jooq.JSONB;
-import org.molgenis.emx2.Row;
 import org.molgenis.emx2.Schema;
 
 public class JsonApi {
@@ -27,24 +25,11 @@ public static void create(Javalin app) {
   public static void getJsonReport(Context ctx) throws JsonProcessingException {
     Schema schema = getSchema(ctx);
     String reports = ctx.queryParam("id");
-    Map<String, Object> parameters = getReportParameters(ctx);
+    Map<String, ?> parameters = getReportParameters(ctx);
     ObjectMapper mapper = new ObjectMapper();
     Map<String, Object> jsonResponse = new HashMap<>();
     for (String reportId : reports.split(",")) {
-      Map<String, String> report = getReportById(reportId, schema);
-      List<Row> rows = schema.retrieveSql(report.get("sql"), parameters);
-      List<Object> result = new ArrayList<>();
-      for (Row row : rows) {
-        // single json object will not be nested in key/value
-        if (rows.get(0).getValueMap().size() == 1
-            && rows.get(0).getValueMap().values().iterator().next() instanceof JSONB) {
-          result.add(
-              mapper.readTree(rows.get(0).getValueMap().values().iterator().next().toString()));
-        } else {
-          result.add(row.getValueMap());
-        }
-        jsonResponse.put(reportId, result);
-      }
+      jsonResponse.put(reportId, getReportAsJson(reportId, schema, parameters));
     }
     if (jsonResponse.size() == 1) {
       ctx.json(jsonResponse.values().iterator().next());
diff --git a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
index 8851da3534..97b6393fa6 100644
--- a/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
+++ b/backend/molgenis-emx2-webapi/src/main/java/org/molgenis/emx2/web/ZipApi.java
@@ -1,12 +1,10 @@
 package org.molgenis.emx2.web;
 
-import static org.molgenis.emx2.graphql.GraphqlSchemaFieldFactory.getReportById;
+import static org.molgenis.emx2.settings.ReportUtils.getReportAsRows;
 import static org.molgenis.emx2.web.Constants.TABLE;
 import static org.molgenis.emx2.web.DownloadApiUtils.includeSystemColumns;
 import static org.molgenis.emx2.web.MolgenisWebservice.getSchema;
 
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
 import io.javalin.Javalin;
 import io.javalin.http.Context;
 import jakarta.servlet.MultipartConfigElement;
@@ -175,15 +173,12 @@ static void getZippedReports(Context ctx) throws IOException {
     }
   }
 
-  static void generateReportsToStore(Context ctx, TableStore store) throws JsonProcessingException {
+  static void generateReportsToStore(Context ctx, TableStore store) {
     String reports = ctx.queryParam("id");
     Schema schema = getSchema(ctx);
     Map<String, ?> parameters = getReportParameters(ctx);
-    String reportsJson = schema.getMetadata().getSetting("reports");
-    List<Map<String, String>> reportList = new ObjectMapper().readValue(reportsJson, List.class);
     for (String reportId : reports.split(",")) {
-      Map<String, String> report = getReportById(reportId, schema);
-      List<Row> rows = schema.retrieveSql(report.get("sql"), parameters);
+      List<Row> rows = getReportAsRows(reportId, schema, parameters);
       if (rows.size() > 0) {
         store.writeTable(reportId, new ArrayList<>(rows.get(0).getColumnNames()), rows);
       } else {
diff --git a/backend/molgenis-emx2-webapi/src/test/java/org.molgenis.emx2.web/WebApiSmokeTests.java b/backend/molgenis-emx2-webapi/src/test/java/org.molgenis.emx2.web/WebApiSmokeTests.java
index f21c2529f2..d6682e4f90 100644
--- a/backend/molgenis-emx2-webapi/src/test/java/org.molgenis.emx2.web/WebApiSmokeTests.java
+++ b/backend/molgenis-emx2-webapi/src/test/java/org.molgenis.emx2.web/WebApiSmokeTests.java
@@ -247,8 +247,8 @@ public void testReports() throws IOException {
             .sessionId(SESSION_ID)
             .get("/pet store reports/api/reports/json?id=report4")
             .asString();
-    jsonbResult = objectMapper.readValue(jsonResults, List.class);
-    assertTrue(jsonbResult.get(0).toString().contains("pooky"));
+    Object result = objectMapper.readValue(jsonResults, Object.class);
+    assertTrue(result.toString().contains("pooky"));
   }
 
   @Test

From 049ef3342e5beb2dc7d5198fc69e544fd4ae76e9 Mon Sep 17 00:00:00 2001
From: mswertz <m.a.swertz@rug.nl>
Date: Thu, 28 Nov 2024 18:47:59 +0100
Subject: [PATCH 13/16] remove unneeded catch

---
 .../graphql/GraphqlSchemaFieldFactory.java    | 22 +++++++------------
 1 file changed, 8 insertions(+), 14 deletions(-)

diff --git a/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java b/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java
index fdcf0da383..749df2d313 100644
--- a/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java
+++ b/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/graphql/GraphqlSchemaFieldFactory.java
@@ -871,20 +871,14 @@ public GraphQLFieldDefinition schemaReportsField(Schema schema) {
         .dataFetcher(
             dataFetchingEnvironment -> {
               Map<String, Object> result = new LinkedHashMap<>();
-              try {
-                final String id = dataFetchingEnvironment.getArgument(ID);
-                Integer offset = dataFetchingEnvironment.getArgumentOrDefault(OFFSET, 0);
-                Integer limit = dataFetchingEnvironment.getArgumentOrDefault(LIMIT, 10);
-                Map<String, String> parameters =
-                    convertKeyValueListToMap(dataFetchingEnvironment.getArgument(PARAMETERS));
-                result.put(DATA, getReportAsJson(id, schema, parameters, limit, offset));
-                result.put(COUNT, getReportCount(id, schema, parameters));
-                return result;
-              } catch (Exception e) {
-                throw new MolgenisException(
-                    "Retrieve of report '" + dataFetchingEnvironment.getArgument(ID) + "' failed ",
-                    e);
-              }
+              final String id = dataFetchingEnvironment.getArgument(ID);
+              Integer offset = dataFetchingEnvironment.getArgumentOrDefault(OFFSET, 0);
+              Integer limit = dataFetchingEnvironment.getArgumentOrDefault(LIMIT, 10);
+              Map<String, String> parameters =
+                  convertKeyValueListToMap(dataFetchingEnvironment.getArgument(PARAMETERS));
+              result.put(DATA, getReportAsJson(id, schema, parameters, limit, offset));
+              result.put(COUNT, getReportCount(id, schema, parameters));
+              return result;
             })
         .build();
   }

From 77b1ac136fded3a76dd39e1aaa794d15f1ceb50a Mon Sep 17 00:00:00 2001
From: mswertz <m.a.swertz@rug.nl>
Date: Thu, 28 Nov 2024 18:49:12 +0100
Subject: [PATCH 14/16] fix docs

---
 docs/molgenis/use_reports.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/molgenis/use_reports.md b/docs/molgenis/use_reports.md
index e6d96c3322..d699941c1a 100644
--- a/docs/molgenis/use_reports.md
+++ b/docs/molgenis/use_reports.md
@@ -28,12 +28,12 @@ settings under key 'reports', for example:
 [
    {
       "id":"report1",
-      "label":"pet report",
+      "description":"pet report",
       "sql":"select * from \"Pet\""
    },
    {
       "id":"report2",
-      "label":"pet report with parameters",
+      "description":"pet report with parameters",
       "sql":"select * from \"Pet\" p where p.name=ANY(${name:string_array})"
    },
 ]

From 52ad04b6426842c3f4d9a3ebf32a1c016bff0bb0 Mon Sep 17 00:00:00 2001
From: mswertz <m.a.swertz@rug.nl>
Date: Thu, 28 Nov 2024 18:51:18 +0100
Subject: [PATCH 15/16] remove space

---
 .../src/main/java/org/molgenis/emx2/settings/ReportUtils.java    | 1 -
 1 file changed, 1 deletion(-)

diff --git a/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/settings/ReportUtils.java b/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/settings/ReportUtils.java
index f03f072d81..5d5044db30 100644
--- a/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/settings/ReportUtils.java
+++ b/backend/molgenis-emx2-graphql/src/main/java/org/molgenis/emx2/settings/ReportUtils.java
@@ -19,7 +19,6 @@ public static Map<String, String> getReportById(String reportId, Schema schema)
         Optional<Map<String, String>> reportOptional =
             reportList.stream().filter(r -> reportId.equals(r.get("id"))).findFirst();
         if (reportOptional.isPresent()) {
-
           return reportOptional.get();
         }
       }

From 3feba5399af3ea7127a88c1e021b2c77dfc33fe4 Mon Sep 17 00:00:00 2001
From: Morris Swertz <m.a.swertz@rug.nl>
Date: Mon, 2 Dec 2024 15:16:25 +0100
Subject: [PATCH 16/16] Update use_reports.md

---
 docs/molgenis/use_reports.md | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/docs/molgenis/use_reports.md b/docs/molgenis/use_reports.md
index d699941c1a..3c426cf1b0 100644
--- a/docs/molgenis/use_reports.md
+++ b/docs/molgenis/use_reports.md
@@ -56,9 +56,10 @@ it into SQL.
 
 You can also use these reports in scripts, to directly download the results, for example:
 
-* http://myserver.com/schema/api/report/report1
-* http://myserver.com/schema/api/report/report1,report2 (then you get result from two reports)
-* http://myserver.com/schema/api/report/report2,report3?name=pooky,spike (then you get result from two reports using 'name' as parameter)
+* http://<host>/<schema>api/reports/report1
+* http://<host>/<schema>/api/reports/report1,report2 (then you get result from two reports)
+* http://<host>/<schema>/api/reports/report2,report3?name=pooky,spike (then you get result from two reports using 'name' as parameter)
+* https://<host>/<schema>/api/reports/json?id=report3
 
 # Returning JSON so you can use reports as REST like 'get' API
 
@@ -70,4 +71,4 @@ Results in something like:
 ```[{name= ...},{name=...}]```
 
 N.B. when you ask for result from multiple reports you will get a nested result using the report names as keys, i.e.
-```{report1:[{...}], report2:[{...}]}```
\ No newline at end of file
+```{report1:[{...}], report2:[{...}]}```