Remove the dataset import history button and related code.

.gitattributes

@@ -2667,7 +2667,6 @@ study/src/org/labkey/study/model/StudyImpl.java -text
 study/src/org/labkey/study/model/StudyLsidHandler.java -text
 study/src/org/labkey/study/model/StudyManager.java -text
 study/src/org/labkey/study/model/StudySnapshot.java -text
-study/src/org/labkey/study/model/UploadLog.java -text
 study/src/org/labkey/study/model/VisitDataset.java -text
 study/src/org/labkey/study/model/VisitDatasetType.java -text
 study/src/org/labkey/study/model/VisitImpl.java -text

study/resources/schemas/dbscripts/postgresql/study-25.003-25.004.sql

@@ -0,0 +1 @@
+DROP TABLE IF EXISTS study.UploadLog;

study/resources/schemas/dbscripts/sqlserver/study-25.003-25.004.sql

@@ -0,0 +1 @@
+DROP TABLE IF EXISTS study.UploadLog;

study/resources/schemas/study.xml

@@ -1564,18 +1564,6 @@
       <column columnName="Container"/>
     </columns>
   </table>
-  <table tableName="UploadLog" tableDbType="TABLE">
-    <columns>
-      <column columnName="RowId"/>
-      <column columnName="Container"/>
-      <column columnName="Created"/>
-      <column columnName="CreatedBy"/>
-      <column columnName="Description"/>
-      <column columnName="FilePath"/>
-      <column columnName="DatasetId"/>
-      <column columnName="Status"/>
-    </columns>
-  </table>
   <table tableName="ParticipantVisit" tableDbType="TABLE">
     <description>Contains one row per subject/visit combination in the study.  Note that this table is populated dynamically as specimen, assay, and dataset data are loaded, and is guaranteed to always be complete.</description>
     <columns>

study/src/org/labkey/study/StudyModule.java

@@ -42,8 +42,6 @@
 import org.labkey.api.exp.PropertyType;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.exp.property.PropertyService;
-import org.labkey.api.files.FileContentService;
-import org.labkey.api.files.TableUpdaterFileListener;
 import org.labkey.api.message.digest.ReportAndDatasetChangeDigestProvider;
 import org.labkey.api.migration.DatabaseMigrationService;
 import org.labkey.api.migration.DefaultMigrationSchemaHandler;
@@ -228,7 +226,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 25.003;
+        return 25.004;
     }
 
     @Override
@@ -391,8 +389,6 @@ protected void startupAfterSpringConfig(ModuleContext moduleContext)
             folderRegistry.addFactories(new StudyWriterFactory(), new StudyImporterFactory());
         }
 
-        FileContentService.get().addFileListener(new TableUpdaterFileListener(StudySchema.getInstance().getTableInfoUploadLog(), "FilePath", TableUpdaterFileListener.Type.filePath, "RowId"));
-
         DatasetDefinition.cleanupOrphanedDatasetDomains();
 
         OptionalFeatureService.get().addExperimentalFeatureFlag(StudyQuerySchema.EXPERIMENTAL_STUDY_SUBSCHEMAS, "Use sub-schemas in Study",

study/src/org/labkey/study/StudySchema.java

@@ -128,11 +128,6 @@ public TableInfo getTableInfoParticipantVisit()
         return getSchema().getTable("ParticipantVisit");
     }
 
-    public TableInfo getTableInfoUploadLog()
-    {
-        return getSchema().getTable("UploadLog");
-    }
-
     public TableInfo getTableInfoCohort()
     {
         return getSchema().getTable("Cohort");

study/src/org/labkey/study/assay/StudyPublishManager.java

@@ -18,13 +18,11 @@
 
 import org.apache.commons.beanutils.ConvertUtils;
 import org.apache.commons.collections4.MapUtils;
-import org.apache.commons.io.IOUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.assay.AbstractAssayProvider;
-import org.labkey.api.assay.AssayFileWriter;
 import org.labkey.api.assay.AssayProtocolSchema;
 import org.labkey.api.assay.AssayProvider;
 import org.labkey.api.assay.AssayService;
@@ -113,9 +111,7 @@
 import org.labkey.api.study.publish.StudyDatasetLinkedColumn;
 import org.labkey.api.study.publish.StudyPublishService;
 import org.labkey.api.study.query.PublishResultsQueryView;
-import org.labkey.api.util.DateUtil;
 import org.labkey.api.util.FileStream;
-import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Pair;
 import org.labkey.api.util.StringExpressionFactory;
@@ -134,16 +130,12 @@
 import org.labkey.study.model.DatasetDomainKind;
 import org.labkey.study.model.StudyImpl;
 import org.labkey.study.model.StudyManager;
-import org.labkey.study.model.UploadLog;
 import org.labkey.study.query.StudyQuerySchema;
 import org.springframework.beans.MutablePropertyValues;
 
 import java.io.Closeable;
 import java.io.IOException;
-import java.io.OutputStream;
 import java.math.BigDecimal;
-import java.nio.file.Files;
-import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -179,12 +171,6 @@ public synchronized static StudyPublishManager getInstance()
         return (StudyPublishManager) StudyPublishService.get();
     }
 
-
-    private TableInfo getTinfoUpdateLog()
-    {
-        return StudySchema.getInstance().getTableInfoUploadLog();
-    }
-
     /**
      * Studies that the user has permission to.
      */
@@ -932,71 +918,16 @@ private static String createUniqueDatasetName(Study study, String assayName)
         return name;
     }
 
-    public UploadLog saveUploadData(User user, Dataset dsd, FileStream tsv, String filename) throws IOException
-    {
-        PipeRoot pipelineRoot = PipelineService.get().findPipelineRoot(dsd.getContainer());
-        if (null == pipelineRoot || !pipelineRoot.isValid())
-            throw new IOException("Please have your administrator set up a pipeline root for this folder.");
-
-        Path dir = pipelineRoot.resolveToNioPath(AssayFileWriter.DIR_NAME);
-        if (null == dir)
-            throw new IOException("Cannot create directory uploaded data: " + AssayFileWriter.DIR_NAME);
-
-        if (!Files.exists(dir))
-        {
-            FileUtil.createDirectory(dir);
-        }
-
-        //File name is studyname_datasetname_date_hhmm.ss
-        Date dateCreated = new Date();
-        String dateString = DateUtil.formatDateTime(dateCreated, "yyy-MM-dd-HHmm");
-        int id = 0;
-        Path file;
-        do
-        {
-            String extension = Objects.toString(filename == null ? "tsv" : FileUtil.getExtension(filename), "tsv");
-            String extra = id++ == 0 ? "" : String.valueOf(id);
-            String fileName = dsd.getStudy().getLabel() + "-" + dsd.getLabel() + "-" + dateString + extra + "." + extension;
-            fileName = fileName.replace('\\', '_').replace('/', '_').replace(':', '_');
-            file = FileUtil.appendName(dir, fileName);
-        }
-        while (Files.exists(file));
-
-        try (OutputStream out = Files.newOutputStream(file))
-        {
-            IOUtils.copy(tsv.openInputStream(), out);
-            tsv.closeInputStream();
-        }
-
-        UploadLog ul = new UploadLog();
-        ul.setContainer(dsd.getContainer());
-        ul.setDatasetId(dsd.getDatasetId());
-        ul.setCreated(dateCreated);
-        ul.setUserId(user.getUserId());
-        ul.setStatus("Initializing");
-        String filePath = FileUtil.hasCloudScheme(file) ? FileUtil.pathToString(file) : file.toFile().getPath();
-        ul.setFilePath(filePath);
-
-        return Table.insert(user, getTinfoUpdateLog(), ul);
-    }
-
-
     /**
-     * Return an array of LSIDs from the newly created dataset entries,
-     * along with the upload log.
+     * Return an array of LSIDs from the newly created dataset entries.
      */
-    public Pair<List<String>, UploadLog> importDatasetTSV(User user, StudyImpl study, DatasetDefinition dsd, DataLoader dl, LookupResolutionType lookupResolutionType, FileStream fileIn, String originalFileName, Map<String, String> columnMap, BatchValidationException errors, QueryUpdateService.InsertOption insertOption, @Nullable AuditBehaviorType auditBehaviorType)
+    public List<String> importDatasetTSV(User user, StudyImpl study, DatasetDefinition dsd, DataLoader dl, LookupResolutionType lookupResolutionType, FileStream fileIn, String originalFileName, Map<String, String> columnMap, BatchValidationException errors, QueryUpdateService.InsertOption insertOption, @Nullable AuditBehaviorType auditBehaviorType)
     {
         DbScope scope = StudySchema.getInstance().getScope();
-
-        UploadLog ul = null;
         List<String> lsids = Collections.emptyList();
 
         try
         {
-            if (null != fileIn)
-                ul = saveUploadData(user, dsd, fileIn, originalFileName);
-
             try (DbScope.Transaction transaction = scope.ensureTransaction())
             {
                 Long defaultQCStateId = study.getDefaultDirectEntryQCState();
@@ -1020,45 +951,9 @@ public Pair<List<String>, UploadLog> importDatasetTSV(User user, StudyImpl study
         catch (IOException x)
         {
             errors.addRowError(new ValidationException("Exception: " + x.getMessage()));
-            if (ul != null)
-            {
-                ul.setStatus("ERROR");
-                String description = ul.getDescription();
-                ul.setDescription(description == null ? "" : description + "\n" + new Date() + ":" + x.getMessage());
-                ul = Table.update(user, StudySchema.getInstance().getTableInfoUploadLog(), ul, ul.getRowId());
-                return Pair.of(lsids, ul);
-            }
         }
 
-        if (!errors.hasErrors())
-        {
-            //Update the status
-            assert ul != null : "Upload log should always exist if no errors have occurred.";
-            ul.setStatus("SUCCESS");
-            ul = Table.update(user, getTinfoUpdateLog(), ul, ul.getRowId());
-        }
-        else if (ul != null)
-        {
-            ul.setStatus("ERROR");
-            StringBuilder sb = new StringBuilder();
-            String sep = "";
-            for (ValidationException e : errors.getRowErrors())
-            {
-                sb.append(sep).append(e.getMessage());
-                sep = "\n";
-            }
-            ul.setDescription(sb.toString());
-            ul = Table.update(user, getTinfoUpdateLog(), ul, ul.getRowId());
-        }
-        return Pair.of(lsids, ul);
-    }
-
-    public UploadLog getUploadLog(Container c, int id)
-    {
-        SimpleFilter filter = SimpleFilter.createContainerFilter(c);
-        filter.addCondition(FieldKey.fromParts("rowId"), id);
-
-        return new TableSelector(getTinfoUpdateLog(), filter, null).getObject(UploadLog.class);
+        return lsids;
     }
 
     @Override

study/src/org/labkey/study/controllers/StudyController.java

@@ -90,7 +90,6 @@
 import org.labkey.api.data.RuntimeSQLException;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.ShowRows;
-import org.labkey.api.data.SimpleDisplayColumn;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.Sort;
 import org.labkey.api.data.SqlExecutor;
@@ -210,7 +209,6 @@
 import org.labkey.api.util.XmlBeansUtil;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.DataView;
-import org.labkey.api.view.GridView;
 import org.labkey.api.view.HtmlView;
 import org.labkey.api.view.HttpView;
 import org.labkey.api.view.JspView;
@@ -227,7 +225,6 @@
 import org.labkey.api.view.template.EmptyView;
 import org.labkey.api.view.template.PageConfig;
 import org.labkey.api.writer.FileSystemFile;
-import org.labkey.api.writer.HtmlWriter;
 import org.labkey.api.writer.VirtualFile;
 import org.labkey.data.xml.TablesDocument;
 import org.labkey.study.CohortFilterFactory;
@@ -265,7 +262,6 @@
 import org.labkey.study.model.StudyImpl;
 import org.labkey.study.model.StudyManager;
 import org.labkey.study.model.StudySnapshot;
-import org.labkey.study.model.UploadLog;
 import org.labkey.study.model.VisitDataset;
 import org.labkey.study.model.VisitDatasetType;
 import org.labkey.study.model.VisitImpl;
@@ -2712,19 +2708,19 @@ protected int importData(DataLoader dl, FileStream file, String originalName, Ba
                 columnMap.put(_form.getSequenceNum(), column);
             }
 
-            Pair<List<String>, UploadLog> result = StudyPublishManager.getInstance().importDatasetTSV(getUser(), _study, _def, dl, getLookupResolutionType(), file, originalName, columnMap, errors, _form.getInsertOption(), auditBehaviorType);
+            List<String> lsids = StudyPublishManager.getInstance().importDatasetTSV(getUser(), _study, _def, dl, getLookupResolutionType(), file, originalName, columnMap, errors, _form.getInsertOption(), auditBehaviorType);
 
-            if (!result.getKey().isEmpty())
+            if (!lsids.isEmpty())
             {
                 // Log the import when SUMMARY is configured, if DETAILED is configured the DetailedAuditLogDataIterator will handle each row change.
                 // It would be nice in the future to replace the DetailedAuditLogDataIterator with a general purpose AuditLogDataIterator
                 // that can delegate the audit behavior type to the AuditDataHandler, so this code can go away
                 //
-                String comment = "Dataset data imported. " + result.getKey().size() + " rows imported";
-                new DatasetDefinition.DatasetAuditHandler(_def).addAuditEvent(getUser(), getContainer(), AuditBehaviorType.SUMMARY, comment, result.getValue());
+                String comment = "Dataset data imported. " + lsids.size() + " rows imported";
+                new DatasetDefinition.DatasetAuditHandler(_def).addAuditEvent(getUser(), getContainer(), AuditBehaviorType.SUMMARY, comment);
             }
 
-            return result.getKey().size();
+            return lsids.size();
         }
 
         @Override
@@ -2843,66 +2839,6 @@ public void setManifest(String manifest)
         }
     }
 
-    @RequiresPermission(UpdatePermission.class)
-    public class ShowUploadHistoryAction extends SimpleViewAction<IdForm>
-    {
-        String _datasetLabel;
-
-        @Override
-        public ModelAndView getView(IdForm form, BindException errors)
-        {
-            TableInfo tInfo = StudySchema.getInstance().getTableInfoUploadLog();
-            DataRegion dr = new DataRegion();
-            dr.addColumns(tInfo, "RowId,Created,CreatedBy,Status,Description");
-            GridView gv = new GridView(dr, errors);
-            DisplayColumn dc = new SimpleDisplayColumn(null) {
-                @Override
-                public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
-                {
-                    ActionURL url = new ActionURL(DownloadTsvAction.class, ctx.getContainer()).addParameter("id", String.valueOf(ctx.get("RowId")));
-                    out.write(LinkBuilder.labkeyLink("Download Data File", url));
-                }
-            };
-            dr.addDisplayColumn(dc);
-
-            SimpleFilter filter = SimpleFilter.createContainerFilter(getContainer());
-            if (form.getId() != 0)
-            {
-                filter.addCondition(Dataset.DATASET_KEY, form.getId());
-                DatasetDefinition dsd = StudyManager.getInstance().getDatasetDefinition(getStudyRedirectIfNull(), form.getId());
-                if (dsd != null)
-                    _datasetLabel = dsd.getLabel();
-            }
-
-            gv.setFilter(filter);
-            return gv;
-        }
-
-        @Override
-        public void addNavTrail(NavTree root)
-        {
-            root.addChild("Upload History" + (null != _datasetLabel ? " for " + _datasetLabel : ""));
-        }
-    }
-
-    @RequiresPermission(UpdatePermission.class)
-    public static class DownloadTsvAction extends SimpleViewAction<IdForm>
-    {
-        @Override
-        public ModelAndView getView(IdForm form, BindException errors) throws Exception
-        {
-            UploadLog ul = StudyPublishManager.getInstance().getUploadLog(getContainer(), form.getId());
-            PageFlowUtil.streamFile(getViewContext().getResponse(), new File(ul.getFilePath()).toPath(), true);
-
-            return null;
-        }
-
-        @Override
-        public void addNavTrail(NavTree root)
-        {
-        }
-    }
-
     @RequiresPermission(ReadPermission.class)
     public static class DatasetItemDetailsAction extends SimpleViewAction<SourceLsidForm>
     {

study/src/org/labkey/study/dataset/DatasetSnapshotProvider.java

@@ -487,7 +487,7 @@ public synchronized ActionURL updateSnapshot(QuerySnapshotForm form, BindExcepti
 
                                 ViewContext context = form.getViewContext();
                                 new DatasetDefinition.DatasetAuditHandler(dsDef).addAuditEvent(context.getUser(), context.getContainer(), AuditBehaviorType.DETAILED,
-                                        "Dataset snapshot was updated. " + numRowsDeleted + " rows were removed and replaced with " + newRows.size() + " rows.", null);
+                                        "Dataset snapshot was updated. " + numRowsDeleted + " rows were removed and replaced with " + newRows.size() + " rows.");
 
                                 def.setLastUpdated(new Date());
                                 def.save(form.getViewContext().getUser());
@@ -504,7 +504,7 @@ public synchronized ActionURL updateSnapshot(QuerySnapshotForm form, BindExcepti
                 {
                     ViewContext context = form.getViewContext();
                     new DatasetDefinition.DatasetAuditHandler(dsDef).addAuditEvent(context.getUser(), context.getContainer(), AuditBehaviorType.DETAILED,
-                            "Dataset snapshot was not updated. Cause of failure: " + e.getMessage(), null);
+                            "Dataset snapshot was not updated. Cause of failure: " + e.getMessage());
                 }
             }
         }
@@ -791,7 +791,7 @@ public void run()
                         DatasetDefinition dsDef = StudyManager.getInstance().getDatasetDefinitionByName(study, _def.getName());
                         if (dsDef != null)
                             new DatasetDefinition.DatasetAuditHandler(dsDef).addAuditEvent(context.getUser(), context.getContainer(), AuditBehaviorType.DETAILED,
-                                    "Dataset snapshot was not updated. Cause of failure: " + errors.getMessage(), null);
+                                    "Dataset snapshot was not updated. Cause of failure: " + errors.getMessage());
                     }
                 }
             }