Merge branch 'master' of github.com:phac-nml/irida

COMBAT-TB · Aug 17, 2020 · 97667f2 · 97667f2
2 parents 2e49e48 + 8c19c88
commit 97667f2
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,12 @@ Changes
 --------------
 * [UI]: Fixed bug when creating/modifying a metadata template the user could not search for a field. (20.05.1)
 * [UI]: Fixed bug where managers could not load Users listing page. (20.05.1)
+* [UI]: Fixed issue where analysis results pages would hang after running with remote synchronized data. (20.05.2)
+* [Developer]: Updated chromedriver to version `latest`. (20.05.2)
+* [UI]: Updated importing numbers through excel file.  IRIDA will now check for excel formatted numeric cells and keep the formatting. (20.05.3);
+* [UI]: Updated sample details metadata so that long values will be broken up over multiple lines. (20.05.3);
+* [UI]: Fixed bug where import bulk metadata button was displayed on linelist page for project collaborators. (20.05.04)
+* [UI]: Fixed bug where add member to project button was displayed on project members page for project collaborators. (20.05.04)
 
 20.01 to 20.05
 --------------

diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 	<groupId>ca.corefacility.bioinformatics</groupId>
 	<artifactId>irida</artifactId>
 	<packaging>war</packaging>
-	<version>20.05.1</version>
+	<version>20.05.4</version>
 	<name>irida</name>
 	<url>http://www.irida.ca</url>
 

diff --git a/src/main/java/ca/corefacility/bioinformatics/irida/model/remote/RemoteStatus.java b/src/main/java/ca/corefacility/bioinformatics/irida/model/remote/RemoteStatus.java
@@ -65,7 +65,7 @@ public class RemoteStatus {
 	private Date lastUpdate;
 
 	@SuppressWarnings("unused")
-	private RemoteStatus() {
+	protected RemoteStatus() {
 	}
 
 	public RemoteStatus(String url, RemoteAPI api) {

diff --git a/...ility/bioinformatics/irida/ria/web/projects/metadata/ProjectSampleMetadataController.java b/...ility/bioinformatics/irida/ria/web/projects/metadata/ProjectSampleMetadataController.java
@@ -132,14 +132,27 @@ public SampleMetadataStorage createProjectSampleMetadata(HttpSession session, @P
 				Iterator<Cell> cellIterator = row.cellIterator();
 				while (cellIterator.hasNext()) {
 					Cell cell = cellIterator.next();
+
 					int columnIndex = cell.getColumnIndex();
 					if (columnIndex < headers.size()) {
 						String header = headers.get(columnIndex);
 
 						if (!Strings.isNullOrEmpty(header)) {
 							// Need to ignore empty headers.
-							cell.setCellType(CellType.STRING);
-							rowMap.put(header, cell.getStringCellValue());
+							if(cell.getCellTypeEnum().equals(CellType.NUMERIC)) {
+								/*
+								This is a special handler for number cells.  It was requested that numbers
+								keep their formatting from their excel files.  E.g. 2.222222 with formatting
+								for 2 decimal places will be saved as 2.22.
+								 */
+								DataFormatter formatter = new DataFormatter();
+								String value = formatter.formatCellValue(cell);
+								rowMap.put(header, value);
+							}
+							else {
+								cell.setCellType(CellType.STRING);
+								rowMap.put(header, cell.getStringCellValue());
+							}
 						}
 					}
 				}

diff --git a/src/main/webapp/package.json b/src/main/webapp/package.json
@@ -99,7 +99,7 @@
     "babel-loader": "^8.1.0",
     "babel-plugin-import": "^1.13.0",
     "bootstrap-sass": "^3.3.7",
-    "chromedriver": "^79.0.0",
+    "chromedriver": "latest",
     "clean-webpack-plugin": "^3.0.0",
     "css-loader": "^3.5.2",
     "cssnano": "^4.1.10",

diff --git a/src/main/webapp/pages/samples/sample.html b/src/main/webapp/pages/samples/sample.html
@@ -4,6 +4,11 @@
       data-layout-decorate="~{samples/_base}">
 <head>
     <title th:text="#{samples.title(${sample.label})}">THIS IS SOMETHING WRONG</title>
+    <style>
+        dd {
+            word-wrap: break-word;
+        }
+    </style>
 </head>
 <body>
 <main layout:fragment="main">

diff --git a/src/main/webapp/resources/js/components/project-members/ProjectMembersTable.jsx b/src/main/webapp/resources/js/components/project-members/ProjectMembersTable.jsx
@@ -69,7 +69,11 @@ export function ProjectMembersTable() {
 
   return (
     <PagedTable
-      buttons={[<AddMembersButton key="add-members-btn" />]}
+      buttons={[
+        window.PAGE.canManage ? (
+          <AddMembersButton key="add-members-btn" />
+        ) : null,
+      ]}
       columns={columns}
     />
   );

diff --git a/src/main/webapp/resources/js/pages/projects/linelist/components/Toolbar/Toolbar.jsx b/src/main/webapp/resources/js/pages/projects/linelist/components/Toolbar/Toolbar.jsx
@@ -8,7 +8,7 @@ import { AddSamplesToCartButton } from "../AddToCartButton/AddSamplesToCart";
 import { Button, Form, Input, Popover } from "antd";
 import {
   IconCloudUpload,
-  IconQuestion
+  IconQuestion,
 } from "../../../../../components/icons/Icons";
 
 const LineListTour = React.lazy(() => import("../Tour/LineListTour"));
@@ -72,20 +72,26 @@ export class ToolbarComponent extends Component {
         </div>
         <div className="toolbar-group">
           <Form layout="inline">
-            <Form.Item>
-              <Button href={urls.import} tour="tour-import">
-                <IconCloudUpload />
-                {i18n("linelist.importBtn.text")}
-              </Button>
-            </Form.Item>
+            {window.project.canManage ? (
+              <Form.Item>
+                <Button
+                  className="t-import-metadata-btn"
+                  href={urls.import}
+                  tour="tour-import"
+                >
+                  <IconCloudUpload />
+                  {i18n("linelist.importBtn.text")}
+                </Button>
+              </Form.Item>
+            ) : null}
             <Form.Item>
               <Search
                 tour="tour-search"
-                onKeyUp={e => this.props.updateFilter(e.target.value)}
+                onKeyUp={(e) => this.props.updateFilter(e.target.value)}
                 id="js-table-filter"
                 className="table-filter t-table-filter"
                 style={{
-                  width: 200
+                  width: 200,
                 }}
               />
             </Form.Item>
@@ -103,7 +109,7 @@ export class ToolbarComponent extends Component {
                   <strong
                     style={{
                       borderBottom: "2px solid orange",
-                      cursor: "pointer"
+                      cursor: "pointer",
                     }}
                     onClick={this.closePopover}
                   >
@@ -136,13 +142,13 @@ ToolbarComponent.propTypes = {
   exportCSV: PropTypes.func.isRequired,
   exportXLSX: PropTypes.func.isRequired,
   scrollTableToTop: PropTypes.func.isRequired,
-  updateFilter: PropTypes.func.isRequired
+  updateFilter: PropTypes.func.isRequired,
 };
 
-const mapStateToProps = state => ({});
+const mapStateToProps = (state) => ({});
 
-const mapDispatchToProps = dispatch => ({
-  updateFilter: value => dispatch(entryActions.setGlobalFilter(value))
+const mapDispatchToProps = (dispatch) => ({
+  updateFilter: (value) => dispatch(entryActions.setGlobalFilter(value)),
 });
 
 export const Toolbar = connect(

diff --git a/src/main/webapp/resources/js/pages/projects/linelist/components/Tour/steps.js b/src/main/webapp/resources/js/pages/projects/linelist/components/Tour/steps.js
@@ -10,7 +10,7 @@ export const steps = [
           <p>{i18n("linelist.tour.table.content")}</p>
         </div>
       );
-    }
+    },
   },
   {
     selector: ".ag-header-cell:nth-of-type(2)",
@@ -32,7 +32,7 @@ export const steps = [
           </ol>
         </div>
       );
-    }
+    },
   },
   {
     selector: `[tour="tour-columns"]`,
@@ -48,7 +48,7 @@ export const steps = [
           <p>{i18n("linelist.tour.columns.content.end")}</p>
         </div>
       );
-    }
+    },
   },
   {
     selector: `.ag-body-viewport-wrapper .ag-row:nth-of-type(1) .ag-cell:nth-of-type(1)`,
@@ -61,7 +61,7 @@ export const steps = [
           <p>{i18n("linelist.tour.edit.content.cancel")}</p>
         </div>
       );
-    }
+    },
   },
   {
     selector: `[tour="tour-search"]`,
@@ -72,7 +72,7 @@ export const steps = [
           <p>{i18n("linelist.tour.search.content")}</p>
         </div>
       );
-    }
+    },
   },
   {
     selector: `[tour="tour-filter-counts"]`,
@@ -84,7 +84,7 @@ export const steps = [
           <p>{i18n("linelist.tour.filterCounts.content.example")}</p>
         </div>
       );
-    }
+    },
   },
   {
     selector: `[tour="tour-export"]`,
@@ -95,23 +95,32 @@ export const steps = [
           <p>{i18n("linelist.tour.export.content")}</p>
         </div>
       );
-    }
+    },
   },
-  {
-    selector: `[tour="tour-import"]`,
-    content() {
-      return (
-        <div>
-          <strong>{i18n("linelist.tour.import.title")}</strong>
-          <p>{i18n("linelist.tour.import.content.intro")}</p>
-          <ul>
-            <li>{i18n("linelist.tour.import.content.li1")}</li>
-            <li>{i18n("linelist.tour.import.content.li2")}</li>
-          </ul>
-        </div>
-      );
+  (function () {
+    /*
+    Since only managers can import metadata, we need to hide this step if a collaborator
+    is viewing the tour.
+     */
+    if (window.project.canManage) {
+      return {
+        selector: `[tour="tour-import"]`,
+        content() {
+          return (
+            <div>
+              <strong>{i18n("linelist.tour.import.title")}</strong>
+              <p>{i18n("linelist.tour.import.content.intro")}</p>
+              <ul>
+                <li>{i18n("linelist.tour.import.content.li1")}</li>
+                <li>{i18n("linelist.tour.import.content.li2")}</li>
+              </ul>
+            </div>
+          );
+        },
+      };
     }
-  },
+    return null;
+  })(),
   {
     selector: ".ag-row .ag-selection-checkbox:nth-of-type(1)",
     content() {
@@ -121,7 +130,7 @@ export const steps = [
           <p>{i18n("linelist.tour.select.content")}</p>
         </div>
       );
-    }
+    },
   },
   {
     selector: `[tour="tour-counts"]`,
@@ -132,7 +141,7 @@ export const steps = [
           <p>{i18n("linelist.tour.selectCounts.content")}</p>
         </div>
       );
-    }
+    },
   },
   {
     selector: `[tour="tour-cart"]`,
@@ -143,7 +152,7 @@ export const steps = [
           <p>{i18n("linelist.tour.cart.content")}</p>
         </div>
       );
-    }
+    },
   },
   {
     selector: ".js-tour-button",
@@ -153,6 +162,6 @@ export const steps = [
           <strong>{i18n("linelist.tour.end")}</strong>
         </div>
       );
-    }
-  }
-];
+    },
+  },
+].filter((i) => i); // Need to filter out any nulled out values.