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Adopt FileLike for more pipeline APIs (#1130)
1 parent e4f1984 commit 48371d0

7 files changed

Lines changed: 14 additions & 28 deletions

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‎src/org/labkey/targetedms/TargetedMSController.java‎

Lines changed: 3 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -285,7 +285,6 @@
285285
import java.awt.*;
286286
import java.awt.image.BufferedImage;
287287
import java.io.ByteArrayInputStream;
288-
import java.io.File;
289288
import java.io.IOException;
290289
import java.io.InputStream;
291290
import java.io.StringWriter;
@@ -3226,7 +3225,7 @@ private void addSpectrumViews(TargetedMSRun run, VBox vbox, Peptide peptide, Bin
32263225
PipeRoot root = PipelineService.get().getPipelineRootSetting(getContainer());
32273226
if (null != root)
32283227
{
3229-
LocalDirectory localDirectory = LocalDirectory.create(root, MODULE_NAME);
3228+
LocalDirectory localDirectory = LocalDirectory.create(root);
32303229
try
32313230
{
32323231
List<SpeclibReaderException> specLibErrors = new ArrayList<>();
@@ -3936,18 +3935,6 @@ public void setPeptideRepresentative(String[] peptideRepresentative)
39363935
{
39373936
_peptideRepresentative = peptideRepresentative;
39383937
}
3939-
3940-
@Override
3941-
public List<File> getValidatedFiles(Container c)
3942-
{
3943-
List<File> files = super.getValidatedFiles(c);
3944-
List<File> resolvedFiles = new ArrayList<>(files.size());
3945-
for(File file: files)
3946-
{
3947-
resolvedFiles.add(FileUtil.resolveFile(file)); // Strips out ".." and "." from the path
3948-
}
3949-
return resolvedFiles;
3950-
}
39513938
}
39523939

39533940
@RequiresPermission(InsertPermission.class)
@@ -6281,7 +6268,7 @@ public boolean handlePost(ResolveConflictForm resolveConflictForm, BindException
62816268
PipeRoot root = PipelineService.get().getPipelineRootSetting(getContainer());
62826269
if (null != root)
62836270
{
6284-
LocalDirectory localDirectory = LocalDirectory.create(root, MODULE_NAME);
6271+
LocalDirectory localDirectory = LocalDirectory.create(root);
62856272
try
62866273
{
62876274
ChromatogramLibraryUtils.incrementLibraryRevision(getContainer(), getUser(), localDirectory);
@@ -6573,7 +6560,7 @@ public ModelAndView getView(DownloadForm form, BindException errors) throws Exce
65736560
PipeRoot root = PipelineService.get().getPipelineRootSetting(getContainer());
65746561
if (null != root)
65756562
{
6576-
LocalDirectory localDirectory = LocalDirectory.create(root, MODULE_NAME);
6563+
LocalDirectory localDirectory = LocalDirectory.create(root);
65776564
try
65786565
{
65796566
ChromatogramLibraryUtils.writeLibrary(container, getUser(), localDirectory, libraryRevision);

‎src/org/labkey/targetedms/TargetedMSManager.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -116,6 +116,7 @@
116116
import org.labkey.targetedms.query.PeptideManager;
117117
import org.labkey.targetedms.query.PrecursorManager;
118118
import org.labkey.targetedms.query.RepresentativeStateManager;
119+
import org.labkey.vfs.FileLike;
119120

120121
import java.io.IOException;
121122
import java.net.URI;
@@ -144,7 +145,6 @@
144145
import static org.labkey.api.targetedms.TargetedMSService.FOLDER_TYPE_PROP_NAME;
145146
import static org.labkey.api.targetedms.TargetedMSService.FolderType.Library;
146147
import static org.labkey.api.targetedms.TargetedMSService.FolderType.LibraryProtein;
147-
import static org.labkey.api.targetedms.TargetedMSService.MODULE_NAME;
148148
import static org.labkey.targetedms.TargetedMSSchema.TABLE_INSTRUMENT_NICKNAME;
149149

150150
public class TargetedMSManager
@@ -707,7 +707,7 @@ public static Long addRunToQueue(ViewBackgroundInfo info,
707707
XarSource source = new AbstractFileXarSource("Wrap Targeted MS Run", container, user)
708708
{
709709
@Override
710-
public Path getLogFilePath()
710+
public FileLike getLogFilePath()
711711
{
712712
throw new UnsupportedOperationException();
713713
}
@@ -1308,7 +1308,7 @@ public static void deleteRuns(List<Long> runIds, Container c, User user, boolean
13081308
PipeRoot root = PipelineService.get().getPipelineRootSetting(run.getContainer());
13091309
if (null != root)
13101310
{
1311-
LocalDirectory localDirectory = LocalDirectory.create(root, MODULE_NAME);
1311+
LocalDirectory localDirectory = LocalDirectory.create(root);
13121312
try
13131313
{
13141314
RepresentativeStateManager.setRepresentativeState(user, run.getContainer(), localDirectory, run, RunRepresentativeDataState.NotRepresentative);

‎src/org/labkey/targetedms/pipeline/ChromatogramCrawlerJob.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -42,7 +42,7 @@ protected ChromatogramCrawlerJob()
4242
public ChromatogramCrawlerJob(ViewBackgroundInfo info, @NotNull PipeRoot root)
4343
{
4444
super(TargetedMSPipelineProvider.name, info, root);
45-
setLogFile(root.getRootFileLike().resolveChild(FileUtil.makeFileNameWithTimestamp("ChromatogramCrawl", "log")).toNioPathForWrite());
45+
setLogFile(root.getRootFileLike().resolveChild(FileUtil.makeFileNameWithTimestamp("ChromatogramCrawl", "log")));
4646

4747
getLogger().info("Description of key statuses:");
4848
for (Chromatogram.SourceStatus value : Chromatogram.SourceStatus.values())

‎src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java‎

Lines changed: 2 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -34,8 +34,6 @@
3434

3535
import java.util.List;
3636

37-
import static org.labkey.api.targetedms.TargetedMSService.MODULE_NAME;
38-
3937
/**
4038
* Simple wrapper job around a {@link TargetedMSImportTask}.
4139
* User: vsharma
@@ -69,14 +67,14 @@ public TargetedMSImportPipelineJob(ViewBackgroundInfo info, ExpData expData, Sky
6967
if ((_expData.hasFileScheme() && root.isCloudRoot()) || (!_expData.hasFileScheme() && !root.isCloudRoot()))
7068
throw new RuntimeException("Cannot process ExpData when its schema does not match root URI scheme.");
7169

72-
LocalDirectory localDirectory = LocalDirectory.create(root, MODULE_NAME, baseLogFileName,
70+
LocalDirectory localDirectory = LocalDirectory.create(root, baseLogFileName,
7371
null != _expData.getFile() ? _expData.getFile().getParentFile().getPath() : FileUtil.getTempDirectory().getPath());
7472
setLocalDirectory(localDirectory);
7573
setLogFile(localDirectory.determineLogFile());
7674
}
7775

7876
@Override
79-
public TaskPipeline getTaskPipeline()
77+
public TaskPipeline<?> getTaskPipeline()
8078
{
8179
return PipelineJobService.get().getTaskPipeline(new TaskId(TargetedMSImportPipelineJob.class));
8280
}

‎src/org/labkey/targetedms/view/confirmImport.jsp‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -18,6 +18,7 @@
1818
<%@ page import="org.labkey.api.view.ActionURL"%>
1919
<%@ page import="org.labkey.api.view.HttpView"%>
2020
<%@ page import="org.labkey.targetedms.TargetedMSController" %>
21+
<%@ page import="org.labkey.vfs.FileLike" %>
2122
<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
2223
<%@ page extends="org.labkey.api.jsp.JspBase" %>
2324
<%
@@ -51,7 +52,7 @@
5152
</tr>
5253
<labkey:form action="<%=targetURL%>" method="POST">
5354
<input type="hidden" name="path" value="<%= h(form.getPath() )%>" />
54-
<% for (java.io.File file : form.getValidatedFiles(getContainer()))
55+
<% for (FileLike file : form.getValidatedFiles(getContainer()))
5556
{ %>
5657
<tr style="border:1px solid;">
5758
<td>

‎test/src/org/labkey/test/components/targetedms/TargetedMSRunsTable.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -69,7 +69,7 @@ public void deleteRun(String documentName)
6969
if (rowIndex < 0)
7070
fail("Unable to find checkbox for non-existent file: " + documentName);
7171
checkCheckbox(rowIndex);
72-
clickHeaderButtonByText("Delete");
72+
clickHeaderButton("Delete");
7373
getWrapper().clickButton("Confirm Delete");
7474
}
7575

@@ -90,7 +90,7 @@ public void openDialogForDocuments(String buttonText, List<String> documentNames
9090
checkCheckbox(rowIndex);
9191
}
9292

93-
clickHeaderButtonByText(buttonText);
93+
clickHeaderButton(buttonText);
9494
}
9595

9696
public void showAllVersions()

‎test/src/org/labkey/test/tests/targetedms/TargetedMSLinkVersionsTest.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -84,7 +84,7 @@ private void deleteExistingQCRuns()
8484

8585
if (hasRunsToDelete)
8686
{
87-
table.clickHeaderButtonByText("Delete");
87+
table.clickHeaderButton("Delete");
8888
clickButton("Confirm Delete");
8989
}
9090
}

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