Merge branch 'release-23.10.1' into development

CHANGELOG.md

@@ -1,4 +1,9 @@
 # Changelog
+
+# [23.10.1] - 2023/12/07
+* [UI]: Fixed issue where filter inputs required focus when they are opened on the project samples page. See [PR 1503](https://github.com/phac-nml/irida/pull/1503)
+* [UI]: Fixed bug preventing sorting and paging on the project members page. See [PR 1504](https://github.com/phac-nml/irida/pull/1504)
+* [Developer]: Fixed race condition where FastQC file processor would start on incomplete file by filtering out files on non complete sequencing runs. [PR 1506](https://github.com/phac-nml/irida/pull/1506)
 
 ## [23.10] - 2023/10/15
 * [Developer]: Added functionality to delete sequence files from file system when a sequence run is removed. [See PR 1468](https://github.com/phac-nml/irida/pull/1468)

build.gradle.kts

@@ -14,7 +14,7 @@ plugins {
 }
 
 group = "ca.corefacility.bioinformatics"
-version = "23.10"
+version = "23.10.1"
 description = "irida"
 
 java {

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/services/UIProjectMembersService.java

@@ -55,6 +55,14 @@ public UIProjectMembersService(ProjectService projectService, UserService userSe
 	 */
 	public TableResponse<ProjectMemberTableModel> getProjectMembers(Long projectId, TableRequest tableRequest) {
 		Project project = projectService.read(projectId);
+
+		// Special case with the sort column on the name column.  Front end sends "name" which is a combination of first and last name.
+		// Needs to get the name from the User in the ProjectUserJoin, and sort by the first name since that is what is
+		// displayed in the table.
+		if (tableRequest.getSortColumn().equals("name")) {
+			tableRequest.setSortColumn("user.firstName");
+		}
+
 		Page<Join<Project, User>> usersForProject = userService.searchUsersForProject(project, tableRequest.getSearch(),
 				tableRequest.getCurrent(), tableRequest.getPageSize(), tableRequest.getSort());
 		List<ProjectMemberTableModel> members = usersForProject.get().map(join -> {

src/main/java/ca/corefacility/bioinformatics/irida/service/SequencingObjectProcessingService.java

@@ -1,6 +1,7 @@
 package ca.corefacility.bioinformatics.irida.service;
 
 import ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject;
+import ca.corefacility.bioinformatics.irida.model.enums.SequencingRunUploadStatus;
 import ca.corefacility.bioinformatics.irida.processing.FileProcessingChain;
 import ca.corefacility.bioinformatics.irida.repositories.sequencefile.SequencingObjectRepository;
 import ca.corefacility.bioinformatics.irida.service.impl.processor.SequenceFileProcessorLauncher;
@@ -66,6 +67,12 @@ public synchronized void findFilesToProcess() {
 		List<SequencingObject> toProcess = sequencingObjectRepository
 				.getSequencingObjectsWithProcessingState(SequencingObject.ProcessingState.UNPROCESSED);
 
+		// filter out sequencing objects on a SequencingRun that is not in a COMPLETE state
+		toProcess.removeIf(seqObj -> (
+				(seqObj.getSequencingRun() != null) &&
+				(!seqObj.getSequencingRun().getUploadStatus().equals(SequencingRunUploadStatus.COMPLETE))
+		));
+
 		// individually loop through and mark the ones we're going to process.  Looping individually so 2 processes are less likely to write at the same time.
 		Iterator<SequencingObject> iterator = toProcess.iterator();
 

src/main/webapp/resources/js/components/ant.design/PagedTable/PagedTable.jsx

@@ -36,6 +36,7 @@ export function PagedTable({ search = true, buttons, ...props }) {
         {search ? (
           <div>
             <Input
+              className="t-search"
               prefix={<IconSearch style={{ color: grey5 }} />}
               onChange={(e) => onSearch(e.target.value)}
             />

src/main/webapp/resources/js/components/project-members/ProjectMembersTable.jsx

@@ -80,6 +80,7 @@ export function ProjectMembersTable({ projectId }) {
       },
       sorter: stringSorter("name"),
       defaultSortOrder: "ascend",
+      className: "t-user-name",
     },
     {
       title: i18n("ProjectMembersTable.projectRole"),

src/main/webapp/resources/js/pages/projects/samples/components/SamplesTable.jsx

@@ -32,6 +32,12 @@ const { RangePicker } = DatePicker;
  * @constructor
  */
 export function SamplesTable() {
+  const nameInputRef = React.useRef(null);
+  const organismInputRef = React.useRef(null);
+  const collectedByInputRef = React.useRef(null);
+  const createdInputRef = React.useRef(null);
+  const modifiedInputRef = React.useRef(null);
+
   const dispatch = useDispatch();
   const {
     projectId,
@@ -115,106 +121,139 @@ export function SamplesTable() {
     confirm({ closeDropdown: false });
   };
 
+  function determineCurrentRef(filterName) {
+    return filterName === "t-organism-select"
+      ? organismInputRef
+      : filterName === "t-name-select"
+      ? nameInputRef
+      : filterName === "t-collectedBy-select"
+      ? collectedByInputRef
+      : filterName === "t-created-filter"
+      ? createdInputRef
+      : filterName === "t-modified-filter"
+      ? modifiedInputRef
+      : null;
+  }
   const getColumnSearchProps = (
     dataIndex,
     filterName = "",
     placeholder = ""
-  ) => ({
-    filterDropdown: ({
-      setSelectedKeys,
-      selectedKeys,
-      confirm,
-      clearFilters,
-    }) => (
-      <div style={{ padding: 8 }}>
-        <Select
-          className={filterName}
-          mode="tags"
-          placeholder={placeholder}
-          value={selectedKeys[0]}
-          onChange={(e) => {
-            const values = Array.isArray(e) && e.length > 0 ? [e] : e;
-            setSelectedKeys(values);
-            confirm({ closeDropdown: false });
-          }}
-          style={{ marginBottom: 8, display: "block" }}
-        />
-        <Space>
-          <Button
-            disabled={selectedKeys.length === 0 || selectedKeys[0].length === 0}
-            onClick={() => handleClearSearch(clearFilters, confirm)}
-            size="small"
-            style={{ width: 89 }}
-          >
-            {i18n("Filter.clear")}
-          </Button>
-          <Button
-            type="primary"
-            onClick={() => handleSearch(selectedKeys, confirm)}
-            icon={<IconSearch />}
-            size="small"
-            style={{ width: 90 }}
-          >
-            {i18n("Filter.search")}
-          </Button>
-        </Space>
-      </div>
-    ),
-    filterIcon: (filtered) => (
-      <IconSearch style={{ color: filtered ? blue6 : undefined }} />
-    ),
-  });
-
-  const getDateColumnSearchProps = (filterName) => ({
-    filterDropdown: ({
-      setSelectedKeys,
-      selectedKeys,
-      confirm,
-      clearFilters,
-    }) => (
-      <div style={{ padding: 8 }} className={filterName}>
-        <div style={{ marginBottom: 8, display: "block" }}>
-          <RangePicker
+  ) => {
+    const currentRef = determineCurrentRef(filterName);
+    return {
+      onFilterDropdownVisibleChange: (visible) => {
+        if (visible) {
+          setTimeout(() => currentRef.current?.focus(), 100);
+        }
+      },
+      filterDropdown: ({
+        setSelectedKeys,
+        selectedKeys,
+        confirm,
+        clearFilters,
+      }) => (
+        <div style={{ padding: 8 }}>
+          <Select
+            className={filterName}
+            mode="tags"
+            placeholder={placeholder}
             value={selectedKeys[0]}
-            onChange={(dates) => {
-              if (dates !== null) {
-                setSelectedKeys([
-                  [dates[0].startOf("day"), dates[1].endOf("day")],
-                ]);
-                confirm({ closeDropdown: false });
-              } else {
-                handleClearSearch(clearFilters, confirm);
-              }
+            onChange={(e) => {
+              const values = Array.isArray(e) && e.length > 0 ? [e] : e;
+              setSelectedKeys(values);
+              confirm({ closeDropdown: false });
             }}
+            style={{ marginBottom: 8, display: "block" }}
+            ref={currentRef}
           />
+          <Space>
+            <Button
+              disabled={
+                selectedKeys.length === 0 || selectedKeys[0].length === 0
+              }
+              onClick={() => handleClearSearch(clearFilters, confirm)}
+              size="small"
+              style={{ width: 89 }}
+            >
+              {i18n("Filter.clear")}
+            </Button>
+            <Button
+              type="primary"
+              onClick={() => handleSearch(selectedKeys, confirm)}
+              icon={<IconSearch />}
+              size="small"
+              style={{ width: 90 }}
+            >
+              {i18n("Filter.search")}
+            </Button>
+          </Space>
         </div>
-        <Space>
-          <Button
-            disabled={selectedKeys.length === 0}
-            onClick={() => handleClearSearch(clearFilters, confirm)}
-            size="small"
-            style={{ width: 89 }}
-            className="t-clear-btn"
-          >
-            {i18n("Filter.clear")}
-          </Button>
-          <Button
-            type="primary"
-            onClick={() => handleSearch(selectedKeys, confirm)}
-            icon={<IconSearch />}
-            size="small"
-            style={{ width: 90 }}
-            className="t-search-btn"
-          >
-            {i18n("Filter.search")}
-          </Button>
-        </Space>
-      </div>
-    ),
-    filterIcon: (filtered) => (
-      <IconSearch style={{ color: filtered ? blue6 : undefined }} />
-    ),
-  });
+      ),
+      filterIcon: (filtered) => (
+        <IconSearch style={{ color: filtered ? blue6 : undefined }} />
+      ),
+    };
+  };
+
+  const getDateColumnSearchProps = (filterName) => {
+    const currentRef = determineCurrentRef(filterName);
+    return {
+      onFilterDropdownVisibleChange: (visible) => {
+        if (visible) {
+          setTimeout(() => currentRef.current?.focus(), 100);
+        }
+      },
+      filterDropdown: ({
+        setSelectedKeys,
+        selectedKeys,
+        confirm,
+        clearFilters,
+      }) => (
+        <div style={{ padding: 8 }} className={filterName}>
+          <div style={{ marginBottom: 8, display: "block" }}>
+            <RangePicker
+              ref={currentRef}
+              value={selectedKeys[0]}
+              onChange={(dates) => {
+                if (dates !== null) {
+                  setSelectedKeys([
+                    [dates[0].startOf("day"), dates[1].endOf("day")],
+                  ]);
+                  confirm({ closeDropdown: false });
+                } else {
+                  handleClearSearch(clearFilters, confirm);
+                }
+              }}
+            />
+          </div>
+          <Space>
+            <Button
+              disabled={selectedKeys.length === 0}
+              onClick={() => handleClearSearch(clearFilters, confirm)}
+              size="small"
+              style={{ width: 89 }}
+              className="t-clear-btn"
+            >
+              {i18n("Filter.clear")}
+            </Button>
+            <Button
+              type="primary"
+              onClick={() => handleSearch(selectedKeys, confirm)}
+              icon={<IconSearch />}
+              size="small"
+              style={{ width: 90 }}
+              className="t-search-btn"
+            >
+              {i18n("Filter.search")}
+            </Button>
+          </Space>
+        </div>
+      ),
+      filterIcon: (filtered) => (
+        <IconSearch style={{ color: filtered ? blue6 : undefined }} />
+      ),
+    };
+  };
 
   const columns = [
     {
@@ -298,7 +337,10 @@ export function SamplesTable() {
       title: i18n("SamplesTable.Column.collectedBy"),
       dataIndex: ["sample", "collectedBy"],
       sorter: true,
-      ...getColumnSearchProps(["sample", "collectedBy"]),
+      ...getColumnSearchProps(
+        ["sample", "collectedBy"],
+        "t-collectedBy-select"
+      ),
     },
     {
       title: i18n("SamplesTable.Column.created"),

src/test/java/ca/corefacility/bioinformatics/irida/ria/integration/components/AntTable.java

@@ -8,6 +8,7 @@
 import java.util.stream.Collectors;
 
 import org.openqa.selenium.By;
+import org.openqa.selenium.Keys;
 import org.openqa.selenium.WebDriver;
 import org.openqa.selenium.WebElement;
 import org.openqa.selenium.support.FindBy;
@@ -29,6 +30,15 @@ public class AntTable {
 	@FindBy(className = "ant-table-row")
 	List<WebElement> rows;
 
+	@FindBy(css = ".ant-pagination-next button")
+	WebElement nextButton;
+
+	@FindBy(css = ".ant-pagination-prev button")
+	WebElement prevButton;
+
+	@FindBy(css = ".t-search input")
+	WebElement searchInput;
+
 	public static AntTable getTable(WebDriver driver) {
 		return PageFactory.initElements(driver, AntTable.class);
 	}
@@ -89,4 +99,19 @@ private Long getMillisecondsFromDate(String dateStr, DateFormat dateFormat) {
 		}
 	}
 
+	public void goToNextPage() {
+		nextButton.click();
+	}
+
+	public void goToPrevPage() {
+		prevButton.click();
+	}
+
+	public void search(String text) {
+		if (!Strings.isNullOrEmpty(text)) {
+			searchInput.sendKeys(Keys.chord(Keys.CONTROL, "a"), text, Keys.ENTER);
+		} else {
+			searchInput.sendKeys(Keys.chord(Keys.CONTROL, "a"), Keys.BACK_SPACE, Keys.ENTER);
+		}
+	}
 }