fixes for updating column mappings for compressed files, getting cypress tests working again

Author: sagehen03

backend/scripts/test_data.sql

@@ -27,7 +27,8 @@ set @delete_dataset_id = LAST_INSERT_ID();
 insert into role_permissions(permission_id, role_id) values (@approve_upload_id, @reviewer_role_id);
 insert into role_permissions(permission_id, role_id) values (@add_user_id, @reviewer_role_id);
 insert into role_permissions(permission_id, role_id) values (@delete_dataset_id, @reviewer_role_id);
-test_
+
+
 insert into user_roles(user_id, role_id) values (@uploader1_id, @uploader_role_id);
 insert into user_roles(user_id, role_id) values (@uploader2_id, @uploader_role_id);
 insert into user_roles(user_id, role_id) values (@reviewer_user_id, @reviewer_role_id);

cypress/e2e/hermes/hermes-upload-cases.cy.js

@@ -38,7 +38,7 @@ describe('Hermes Upload', {retries: 0}, () => {
     cy.get('#maf').type('1');
     cy.get('#otherFilters').type('My Filters');
 
-    cy.get('input[type="file"]').attachFile('sample-gwas-expanded.csv');
+    cy.get('input[type="file"]').attachFile({ filePath: 'sample-gwas-expanded.csv.gz', encoding: 'binary'});
     cy.get('[data-cy="column-dropdown"]').eq(1).type('chromosome').type('{enter}');
     cy.get('[data-cy="column-dropdown"]').eq(2).type('position').type('{enter}');
     cy.get('[data-cy="column-dropdown"]').eq(3).type('alt').type('{enter}');

cypress/e2e/hermes/hermes-upload.cy.js

@@ -37,7 +37,7 @@ describe('Hermes Upload', {retries: 0}, () => {
     cy.get('#maf').type('1');
     cy.get('#otherFilters').type('My Filters');
 
-    cy.get('input[type="file"]').attachFile('sample-gwas-expanded.csv');
+    cy.get('input[type="file"]').attachFile({ filePath: 'sample-gwas-expanded.csv.gz', encoding: 'binary'});
     cy.get('[data-cy="column-dropdown"]').eq(1).type('chromosome').type('{enter}');
     cy.get('[data-cy="column-dropdown"]').eq(2).type('position').type('{enter}');
     cy.get('[data-cy="column-dropdown"]').eq(3).type('alt').type('{enter}');

cypress/fixtures/sample-gwas-expanded.csv

@@ -82,11 +82,14 @@ const getIcon = (status) => {
     }
 };
 
-// flat array of possible phenotypes
 const uniquePhenotypes = computed(() => {
   return [...new Set(fileUploads.value.map(f => f.phenotype))];
 });
 
+const uniqueAncestry = computed(() => {
+  return [...new Set(fileUploads.value.map(f => f.ancestry))];
+});
+
 // flat array of possible statuses
 const uniqueQCstatuses = computed(() => {
   return [...new Set(fileUploads.value.map(f => f.qc_status))];
@@ -101,6 +104,13 @@ const columns = ref([
     options: uniquePhenotypes,
     sortable: true
   },
+  {
+    header: "Ancestry",
+    field: "ancestry",
+    filterType: "multiSelect",
+    options: uniqueAncestry,
+    sortable: true
+  },
   {
     header: "Dataset",
     field: "dataset_name",
@@ -235,7 +245,7 @@ const filters = ref(
                     <DataTable v-model:filters="filters"
                                filterDisplay="row"
                                :value="fileUploads"
-                               tableStyle="min-width: 50rem"
+                               class="w-full"
                                paginator
                                :rows="20"
                                :loading="tableLoading"