diff --git a/src/org/labkey/targetedms/TargetedMSController.java b/src/org/labkey/targetedms/TargetedMSController.java index a376752e8..3e9a8aefa 100644 --- a/src/org/labkey/targetedms/TargetedMSController.java +++ b/src/org/labkey/targetedms/TargetedMSController.java @@ -285,7 +285,6 @@ import java.awt.*; import java.awt.image.BufferedImage; import java.io.ByteArrayInputStream; -import java.io.File; import java.io.IOException; import java.io.InputStream; import java.io.StringWriter; @@ -3226,7 +3225,7 @@ private void addSpectrumViews(TargetedMSRun run, VBox vbox, Peptide peptide, Bin PipeRoot root = PipelineService.get().getPipelineRootSetting(getContainer()); if (null != root) { - LocalDirectory localDirectory = LocalDirectory.create(root, MODULE_NAME); + LocalDirectory localDirectory = LocalDirectory.create(root); try { List specLibErrors = new ArrayList<>(); @@ -3936,18 +3935,6 @@ public void setPeptideRepresentative(String[] peptideRepresentative) { _peptideRepresentative = peptideRepresentative; } - - @Override - public List getValidatedFiles(Container c) - { - List files = super.getValidatedFiles(c); - List resolvedFiles = new ArrayList<>(files.size()); - for(File file: files) - { - resolvedFiles.add(FileUtil.resolveFile(file)); // Strips out ".." and "." from the path - } - return resolvedFiles; - } } @RequiresPermission(InsertPermission.class) @@ -6281,7 +6268,7 @@ public boolean handlePost(ResolveConflictForm resolveConflictForm, BindException PipeRoot root = PipelineService.get().getPipelineRootSetting(getContainer()); if (null != root) { - LocalDirectory localDirectory = LocalDirectory.create(root, MODULE_NAME); + LocalDirectory localDirectory = LocalDirectory.create(root); try { ChromatogramLibraryUtils.incrementLibraryRevision(getContainer(), getUser(), localDirectory); @@ -6573,7 +6560,7 @@ public ModelAndView getView(DownloadForm form, BindException errors) throws Exce PipeRoot root = PipelineService.get().getPipelineRootSetting(getContainer()); if (null != root) { - LocalDirectory localDirectory = LocalDirectory.create(root, MODULE_NAME); + LocalDirectory localDirectory = LocalDirectory.create(root); try { ChromatogramLibraryUtils.writeLibrary(container, getUser(), localDirectory, libraryRevision); diff --git a/src/org/labkey/targetedms/TargetedMSManager.java b/src/org/labkey/targetedms/TargetedMSManager.java index 46ef668b3..d98366c35 100644 --- a/src/org/labkey/targetedms/TargetedMSManager.java +++ b/src/org/labkey/targetedms/TargetedMSManager.java @@ -116,6 +116,7 @@ import org.labkey.targetedms.query.PeptideManager; import org.labkey.targetedms.query.PrecursorManager; import org.labkey.targetedms.query.RepresentativeStateManager; +import org.labkey.vfs.FileLike; import java.io.IOException; import java.net.URI; @@ -144,7 +145,6 @@ import static org.labkey.api.targetedms.TargetedMSService.FOLDER_TYPE_PROP_NAME; import static org.labkey.api.targetedms.TargetedMSService.FolderType.Library; import static org.labkey.api.targetedms.TargetedMSService.FolderType.LibraryProtein; -import static org.labkey.api.targetedms.TargetedMSService.MODULE_NAME; import static org.labkey.targetedms.TargetedMSSchema.TABLE_INSTRUMENT_NICKNAME; public class TargetedMSManager @@ -707,7 +707,7 @@ public static Long addRunToQueue(ViewBackgroundInfo info, XarSource source = new AbstractFileXarSource("Wrap Targeted MS Run", container, user) { @Override - public Path getLogFilePath() + public FileLike getLogFilePath() { throw new UnsupportedOperationException(); } @@ -1308,7 +1308,7 @@ public static void deleteRuns(List runIds, Container c, User user, boolean PipeRoot root = PipelineService.get().getPipelineRootSetting(run.getContainer()); if (null != root) { - LocalDirectory localDirectory = LocalDirectory.create(root, MODULE_NAME); + LocalDirectory localDirectory = LocalDirectory.create(root); try { RepresentativeStateManager.setRepresentativeState(user, run.getContainer(), localDirectory, run, RunRepresentativeDataState.NotRepresentative); diff --git a/src/org/labkey/targetedms/pipeline/ChromatogramCrawlerJob.java b/src/org/labkey/targetedms/pipeline/ChromatogramCrawlerJob.java index dac4379a5..950139b66 100644 --- a/src/org/labkey/targetedms/pipeline/ChromatogramCrawlerJob.java +++ b/src/org/labkey/targetedms/pipeline/ChromatogramCrawlerJob.java @@ -42,7 +42,7 @@ protected ChromatogramCrawlerJob() public ChromatogramCrawlerJob(ViewBackgroundInfo info, @NotNull PipeRoot root) { super(TargetedMSPipelineProvider.name, info, root); - setLogFile(root.getRootFileLike().resolveChild(FileUtil.makeFileNameWithTimestamp("ChromatogramCrawl", "log")).toNioPathForWrite()); + setLogFile(root.getRootFileLike().resolveChild(FileUtil.makeFileNameWithTimestamp("ChromatogramCrawl", "log"))); getLogger().info("Description of key statuses:"); for (Chromatogram.SourceStatus value : Chromatogram.SourceStatus.values()) diff --git a/src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java b/src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java index 80fc1c053..04b966e11 100644 --- a/src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java +++ b/src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java @@ -34,8 +34,6 @@ import java.util.List; -import static org.labkey.api.targetedms.TargetedMSService.MODULE_NAME; - /** * Simple wrapper job around a {@link TargetedMSImportTask}. * User: vsharma @@ -69,14 +67,14 @@ public TargetedMSImportPipelineJob(ViewBackgroundInfo info, ExpData expData, Sky if ((_expData.hasFileScheme() && root.isCloudRoot()) || (!_expData.hasFileScheme() && !root.isCloudRoot())) throw new RuntimeException("Cannot process ExpData when its schema does not match root URI scheme."); - LocalDirectory localDirectory = LocalDirectory.create(root, MODULE_NAME, baseLogFileName, + LocalDirectory localDirectory = LocalDirectory.create(root, baseLogFileName, null != _expData.getFile() ? _expData.getFile().getParentFile().getPath() : FileUtil.getTempDirectory().getPath()); setLocalDirectory(localDirectory); setLogFile(localDirectory.determineLogFile()); } @Override - public TaskPipeline getTaskPipeline() + public TaskPipeline getTaskPipeline() { return PipelineJobService.get().getTaskPipeline(new TaskId(TargetedMSImportPipelineJob.class)); } diff --git a/src/org/labkey/targetedms/view/confirmImport.jsp b/src/org/labkey/targetedms/view/confirmImport.jsp index 67cdae904..55235c9b7 100644 --- a/src/org/labkey/targetedms/view/confirmImport.jsp +++ b/src/org/labkey/targetedms/view/confirmImport.jsp @@ -18,6 +18,7 @@ <%@ page import="org.labkey.api.view.ActionURL"%> <%@ page import="org.labkey.api.view.HttpView"%> <%@ page import="org.labkey.targetedms.TargetedMSController" %> +<%@ page import="org.labkey.vfs.FileLike" %> <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %> <%@ page extends="org.labkey.api.jsp.JspBase" %> <% @@ -51,7 +52,7 @@ - <% for (java.io.File file : form.getValidatedFiles(getContainer())) + <% for (FileLike file : form.getValidatedFiles(getContainer())) { %> diff --git a/test/src/org/labkey/test/components/targetedms/TargetedMSRunsTable.java b/test/src/org/labkey/test/components/targetedms/TargetedMSRunsTable.java index 232bd34cc..d258d3fb1 100644 --- a/test/src/org/labkey/test/components/targetedms/TargetedMSRunsTable.java +++ b/test/src/org/labkey/test/components/targetedms/TargetedMSRunsTable.java @@ -69,7 +69,7 @@ public void deleteRun(String documentName) if (rowIndex < 0) fail("Unable to find checkbox for non-existent file: " + documentName); checkCheckbox(rowIndex); - clickHeaderButtonByText("Delete"); + clickHeaderButton("Delete"); getWrapper().clickButton("Confirm Delete"); } @@ -90,7 +90,7 @@ public void openDialogForDocuments(String buttonText, List documentNames checkCheckbox(rowIndex); } - clickHeaderButtonByText(buttonText); + clickHeaderButton(buttonText); } public void showAllVersions() diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSLinkVersionsTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSLinkVersionsTest.java index 3a0dc6df6..326a9a95c 100644 --- a/test/src/org/labkey/test/tests/targetedms/TargetedMSLinkVersionsTest.java +++ b/test/src/org/labkey/test/tests/targetedms/TargetedMSLinkVersionsTest.java @@ -84,7 +84,7 @@ private void deleteExistingQCRuns() if (hasRunsToDelete) { - table.clickHeaderButtonByText("Delete"); + table.clickHeaderButton("Delete"); clickButton("Confirm Delete"); } }