Fix merge conflicts

Author: bbimber

SequenceAnalysis/build.gradle

@@ -44,6 +44,7 @@ dependencies {
     BuildUtils.addLabKeyDependency(project: project, config: "apiImplementation", depProjectPath: ":server:modules:LabDevKitModules:laboratory", depProjectConfig: "apiJarFile")
     BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
     BuildUtils.addLabKeyDependency(project: project, config: "apiImplementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
+    BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:discvrcore", depProjectConfig: "apiJarFile")
     BuildUtils.addExternalDependency(
             project,
             new ExternalDependency(

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java

@@ -72,6 +72,7 @@
 import org.labkey.api.data.Table;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
+import org.labkey.api.discvrcore.annotation.UtilityAction;
 import org.labkey.api.exceptions.OptimisticConflictException;
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.exp.api.DataType;
@@ -428,6 +429,81 @@ public void addNavTrail(NavTree tree)
         }
     }
 
+    @RequiresPermission(ReadPermission.class)
+    @IgnoresTermsOfUse
+    public static class DownloadTempImageAction extends ExportAction<TempImageAction>
+    {
+        @Override
+        public void export(TempImageAction form, HttpServletResponse response, BindException errors) throws Exception
+        {
+            File parentDir = form.getDirectory() == null ? FileUtil.getTempDirectory() : new File(FileUtil.getTempDirectory(), form.getDirectory());
+            File targetFile = new File(parentDir, form.getFileName());
+            targetFile = FileUtil.getAbsoluteCaseSensitiveFile(targetFile);
+
+            if (!NetworkDrive.exists(targetFile))
+            {
+                throw new FileNotFoundException("Could not find file: " + targetFile.getPath());
+            }
+
+            if (parentDir.listFiles() == null)
+            {
+                throw new FileNotFoundException("Unable to list the contents of folder: " + parentDir.getPath());
+            }
+
+            PageFlowUtil.streamFile(response, targetFile, false);
+
+            //the file will be recreated, so delete upon running
+            FileUtils.deleteQuietly(targetFile);
+
+            //if the folder if empty, remove it too.  other simultaneous requests might have deleted this folder before we get to it
+            if (parentDir != null && parentDir.exists())
+            {
+                File[] children = parentDir.listFiles();
+                if (children != null && children.length == 0 && !parentDir.equals(FileUtil.getTempDirectory()))
+                {
+                    FileUtils.deleteQuietly(parentDir); //the Images folder
+                    File parent = parentDir.getParentFile();
+                    FileUtils.deleteQuietly(parent); //the file's folder
+
+                    if (parent != null && parent.getParentFile() != null)
+                    {
+                        File[] children2 = parent.getParentFile().listFiles();
+                        if (children2 != null && children2.length == 0)
+                            FileUtils.deleteQuietly(parent.getParentFile()); //the file's folder
+                    }
+                }
+            }
+        }
+    }
+
+    @RequiresPermission(ReadPermission.class)
+    @IgnoresTermsOfUse
+    public static class ConvertTextToFileAction extends ExportAction<ConvertTextToFileForm>
+    {
+        @Override
+        public void export(ConvertTextToFileForm form, HttpServletResponse response, BindException errors) throws Exception
+        {
+            String text = form.getText();
+
+            if (text == null)
+            {
+                errors.reject(ERROR_MSG, "Need to provide text");
+                return;
+            }
+            if (form.getFileName() == null)
+            {
+                errors.reject(ERROR_MSG, "Need to provide a filename");
+                return;
+            }
+
+            Map<String, String> headers = new HashMap<>();
+
+            PageFlowUtil.prepareResponseForFile(response, headers, form.getFileName(), true);
+            response.getOutputStream().print(text);
+        }
+    }
+
+    @UtilityAction(label = "Find Orphan Files", description = "This will start a pipeline job that will inspect all files in this folder to identify potential orphan or otherwise unnecessary files")
     @RequiresPermission(ReadPermission.class)
     public static class FindOrphanFilesAction extends ConfirmAction<Object>
     {
@@ -4955,6 +5031,7 @@ public void setOutputFileIds(Integer[] outputFileIds)
         }
     }
 
+    @UtilityAction(label = "Update ExpData Path", description = "This will update the DataFileUrl on the selected ExpData to the path provided")
     @RequiresSiteAdmin
     public static class UpdateExpDataPathAction extends ConfirmAction<UpdateExpDataPathForm>
     {

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java

@@ -300,6 +300,7 @@ private void processContainer(Container c, Logger log) throws IOException, Pipel
         if (root != null && !root.isCloudRoot())
         {
             //first sequences
+            log.debug("Inspecting sequences");
             File sequenceDir = new File(root.getRootPath(), ".sequences");
             TableInfo tableRefNtSequences = SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_REF_NT_SEQUENCES);
             TableSelector ntTs = new TableSelector(tableRefNtSequences, new SimpleFilter(FieldKey.fromString("container"), c.getId()), null);
@@ -342,6 +343,7 @@ private void processContainer(Container c, Logger log) throws IOException, Pipel
             }
 
             //then libraries
+            log.debug("Inspecting genomes");
             File libraryDir = SequenceAnalysisManager.get().getReferenceLibraryDir(c);
             if (libraryDir != null && libraryDir.exists())
             {
@@ -516,6 +518,7 @@ private void processContainer(Container c, Logger log) throws IOException, Pipel
             }
 
             //finally outputfiles
+            log.debug("Inspecting outputs");
             TableInfo ti = SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_OUTPUTFILES);
             TableSelector ts = new TableSelector(ti, Collections.singleton("dataid"), new SimpleFilter(FieldKey.fromString("container"), c.getId()), null);
             Set<String> expectedFileNames = new HashSet<>();
@@ -563,6 +566,8 @@ private void processContainer(Container c, Logger log) throws IOException, Pipel
                     }
                 }
             }
+
+            log.debug("done");
         }
 
         for (Container child : c.getChildren())

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceProvider.java

@@ -217,30 +217,38 @@ public List<NavItem> getSubjectIdSummary(Container c, User u, String subjectId)
     @Override
     public List<TabbedReportItem> getTabbedReportItems(Container c, User u)
     {
+        if (!c.getActiveModules().contains(getOwningModule()))
+        {
+            return Collections.emptyList();
+        }
+
         List<TabbedReportItem> items = new ArrayList<>();
 
-        NavItem owner = getDataNavItems(c, u).get(0);
+        NavItem owner = getReportItems(c, u).get(0);
         String category = "Sequence Data";
         QueryCache cache = new QueryCache();
 
         TabbedReportItem readsets = new QueryTabbedReportItem(cache, this, SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_READSETS, "Sequence Readsets", category);
         readsets.setOwnerKey(owner.getPropertyManagerKey());
+        readsets.setVisible(owner.isVisible(c, u));
         items.add(readsets);
 
         TabbedReportItem analyses = new QueryTabbedReportItem(cache, this, SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_ANALYSES, "Sequence Analyses", category);
         analyses.setSubjectIdFieldKey(FieldKey.fromString("readset/subjectid"));
         analyses.setSampleDateFieldKey(FieldKey.fromString("readset/sampledate"));
-        analyses.setAllProjectsFieldKey(FieldKey.fromString("readset/allProjectsPivot"));
-        analyses.setOverlappingProjectsFieldKey(FieldKey.fromString("readset/overlappingProjectsPivot"));
+        analyses.setKeyOverride("allProjectsFieldName", FieldKey.fromString("readset/allProjectsPivot"));
+        analyses.setKeyOverride("overlappingProjectsFieldName", FieldKey.fromString("readset/overlappingProjectsPivot"));
         analyses.setOwnerKey(owner.getPropertyManagerKey());
+        analyses.setVisible(owner.isVisible(c, u));
         items.add(analyses);
 
         TabbedReportItem outputs = new QueryTabbedReportItem(cache, this, SequenceAnalysisSchema.SCHEMA_NAME, SequenceAnalysisSchema.TABLE_OUTPUTFILES, "Sequence Outputs", category);
         outputs.setSubjectIdFieldKey(FieldKey.fromString("readset/subjectid"));
         outputs.setSampleDateFieldKey(FieldKey.fromString("readset/sampledate"));
-        outputs.setAllProjectsFieldKey(FieldKey.fromString("readset/allProjectsPivot"));
-        outputs.setOverlappingProjectsFieldKey(FieldKey.fromString("readset/overlappingProjectsPivot"));
+        outputs.setKeyOverride("allProjectsFieldName", FieldKey.fromString("readset/allProjectsPivot"));
+        outputs.setKeyOverride("overlappingProjectsFieldName", FieldKey.fromString("readset/overlappingProjectsPivot"));
         outputs.setOwnerKey(owner.getPropertyManagerKey());
+        outputs.setVisible(owner.isVisible(c, u));
         items.add(outputs);
 
         return items;

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java

@@ -344,6 +344,8 @@ public void getOrphanFilesForContainer(Container c, User u, Set<File> orphanFile
                 return;
             }
 
+
+            getJob().updateStatusForTask();
             if (getJob().isCancelled())
             {
                 throw new CancelledException();

Studies/.gitignore

@@ -0,0 +1 @@
+resources/credits/jars.txt

Studies/api-src/org/labkey/api/studies/StudiesService.java

@@ -1,12 +1,15 @@
 package org.labkey.api.studies;
 
 import org.labkey.api.data.Container;
+import org.labkey.api.data.TableCustomizer;
 import org.labkey.api.module.Module;
 import org.labkey.api.resource.Resource;
 import org.labkey.api.security.User;
+import org.labkey.api.studies.study.EventProvider;
 import org.labkey.api.util.Path;
 
 import java.io.IOException;
+import java.util.List;
 
 /**
  * Created by bimber on 11/3/2016.
@@ -28,4 +31,10 @@ static public void setInstance(StudiesService instance)
     abstract public void importFolderDefinition(Container container, User user, Module m, Path sourceFolderDirPath) throws IOException;
 
     abstract public void loadTsv(Resource tsv, String schemaName, User u, Container c);
+
+    abstract public void registerEventProvider(EventProvider ep);
+
+    abstract public List<EventProvider> getEventProviders(Container c);
+
+    abstract public TableCustomizer getStudiesTableCustomizer();
 }

…udies/query/ResultsOOODisplayColumn.java …udies/query/ResultsOORDisplayColumn.javaStudies/src/org/labkey/studies/query/ResultsOOODisplayColumn.java renamed to Studies/api-src/org/labkey/api/studies/query/ResultsOORDisplayColumn.java Studies/src/org/labkey/studies/query/ResultsOOODisplayColumn.java renamed to Studies/api-src/org/labkey/api/studies/query/ResultsOORDisplayColumn.java

@@ -1,4 +1,4 @@
-package org.labkey.studies.query;
+package org.labkey.api.studies.query;
 
 import org.apache.commons.lang3.StringUtils;
 import org.labkey.api.data.ColumnInfo;
@@ -9,9 +9,9 @@
 import java.text.DecimalFormat;
 import java.util.Set;
 
-public class ResultsOOODisplayColumn extends DataColumn
+public class ResultsOORDisplayColumn extends DataColumn
 {
-    public ResultsOOODisplayColumn(ColumnInfo col)
+    public ResultsOORDisplayColumn(ColumnInfo col)
     {
         super(col);
     }
@@ -48,15 +48,15 @@ public Object getDisplayValue(RenderContext ctx)
 
     private FieldKey getOOR()
     {
-        FieldKey oor = FieldKey.fromString("resultOOOIndicator");
-        if (getBoundColumn() != null)
+        ColumnInfo col = getBoundColumn();
+        if (col == null)
         {
-            return FieldKey.fromParts(getBoundColumn().getFieldKey().getParent(), oor);
-        }
-        else
-        {
-            return oor;
+            return null;
         }
+
+        FieldKey oor = FieldKey.fromString(col.getFieldKey().getName() + "OORIndicator");
+
+        return getBoundColumn().getFieldKey().getParent() == null ? oor : FieldKey.fromParts(getBoundColumn().getFieldKey().getParent(), oor);
     }
 
     @Override

Studies/api-src/org/labkey/api/studies/study/AbstractEventProvider.java

@@ -0,0 +1,88 @@
+package org.labkey.api.studies.study;
+
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.module.Module;
+import org.labkey.api.query.QueryService;
+import org.labkey.api.query.UserSchema;
+import org.labkey.api.security.User;
+import org.labkey.api.security.permissions.ReadPermission;
+
+import java.util.Collection;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Map;
+
+public abstract class AbstractEventProvider implements EventProvider
+{
+    private final String _name;
+    private final String _label;
+    private final String _description;
+    private final Module _owner;
+
+    public AbstractEventProvider(String name, String label, String description, Module owner)
+    {
+        _name = name;
+        _label = label;
+        _description = description;
+        _owner = owner;
+    }
+
+    @Override
+    public String getDescription()
+    {
+        return _description;
+    }
+
+    @Override
+    public String getLabel()
+    {
+        return _label;
+    }
+
+    @Override
+    public String getName()
+    {
+        return _name;
+    }
+
+    @Override
+    public boolean isAvailable(Container c)
+    {
+        return c.getActiveModules().contains(_owner);
+    }
+
+    @Override
+    public final Map<String, Date> inferDates(Collection<String> subjectList, Container c, User u)
+    {
+        Map<String, Date> result = new HashMap<>(inferDatesRaw(subjectList, c, u));
+        subjectList.forEach(x -> {
+            if (!result.containsKey(x))
+            {
+                result.put(x, null);
+            }
+        });
+
+        return result;
+    }
+
+    abstract protected Map<String, Date> inferDatesRaw(Collection<String> subjectList, Container c, User u);
+
+    protected @Nullable TableInfo getTable(Container c, User u, String schema, String table)
+    {
+        UserSchema us = QueryService.get().getUserSchema(u, c, schema);
+        if (us == null)
+        {
+            return null;
+        }
+
+        TableInfo ti = us.getTable("assignment");
+        if (ti == null || !ti.hasPermission(u, ReadPermission.class))
+        {
+            return null;
+        }
+
+        return ti;
+    }
+}

Studies/api-src/org/labkey/api/studies/study/EventProvider.java

@@ -0,0 +1,26 @@
+package org.labkey.api.studies.study;
+
+import org.labkey.api.data.Container;
+import org.labkey.api.security.User;
+
+import java.util.Collection;
+import java.util.Date;
+import java.util.Map;
+
+/**
+ * Each study will have a handful of important dates, which are used to define relative dates for each subject/participant.
+ * The EventProvider classes provide a code-based way to establish the handful of critical dates. This code is executed to populate
+ * the KeyEvents table, which maps subject/event to date.
+ */
+public interface EventProvider
+{
+    boolean isAvailable(Container c);
+
+    String getName();
+
+    String getLabel();
+
+    String getDescription();
+
+    Map<String, Date> inferDates(Collection<String> subjectList, Container c, User u);
+}