Expose more PropertyDescriptor data in exp.Fields (#7130)

Author: labkey-jeckels

api/src/org/labkey/api/reports/report/r/view/DownloadParamReplacement.java

@@ -19,6 +19,7 @@
 import org.labkey.api.reports.report.ScriptOutput;
 import org.labkey.api.reports.report.r.AbstractParamReplacement;
 import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.Path;
 
 import java.io.File;
 
@@ -49,7 +50,7 @@ protected final File getSubstitution(File directory, String extension)
                 fileName = getName().concat(extension);
 
             if (directory != null)
-                file = FileUtil.appendName(directory, fileName);
+                file = FileUtil.appendPath(directory, Path.parse(fileName));
         }
         if (file != null)
             addFile(file);

assay/src/org/labkey/assay/AssayIntegrationTestCase.jsp

@@ -96,6 +96,8 @@
 <%@ page import="java.io.IOException" %>
 <%@ page import="org.apache.commons.collections.MapUtils" %>
 <%@ page import="org.labkey.vfs.FileSystemLike" %>
+<%@ page import="static org.junit.Assert.assertEquals" %>
+<%@ page import="static org.junit.Assert.assertNotEquals" %>
 
 <%@ page extends="org.labkey.api.jsp.JspTest.BVT" %>
 <%!
@@ -559,18 +561,18 @@
         runsQUS.updateRows(user, c, Collections.singletonList(updated), null, errors, null, null);
         // verify runs modified is changed, but created is not
         Map<String, Object> modifiedRunResults = new TableSelector(runsTable, selectColumns, new SimpleFilter("rowId", runRowId), null).getMap();
-        assertTrue(modifiedRunResults.get("Created").equals(runOriginalCreated));
-        assertFalse(modifiedRunResults.get("Modified").equals(runOriginalModified));
+        assertEquals("modifiedRunResults should have the same Created", modifiedRunResults.get("Created"), runOriginalCreated);
+        assertNotEquals("modifiedRunResults should have a different Modified", modifiedRunResults.get("Modified"), runOriginalModified);
 
         // verify results created/modified matches run's created in query table
         Map<String, Object> queryResultAfterRunModify = new TableSelector(resultsTable, selectColumns, new SimpleFilter(runFieldKey, runRowId), null).getMap();
-        assertTrue(queryResultAfterRunModify.get("Created").equals(runOriginalCreated));
-        assertTrue(queryResultAfterRunModify.get("Modified").equals(runOriginalCreated));
-        assertFalse(queryResultAfterRunModify.get("Modified").equals(modifiedRunResults.get("Modified")));
+        assertEquals("queryResultAfterRunModify should have the same Created", queryResultAfterRunModify.get("Created"), runOriginalCreated);
+        assertEquals("queryResultAfterRunModify should have the same Modified", queryResultAfterRunModify.get("Modified"), runOriginalCreated);
+        assertNotEquals("queryResultAfterRunModify should have a different Modified", queryResultAfterRunModify.get("Modified"), modifiedRunResults.get("Modified"));
 
         // verify created/modified in provisioned result table is still not populated after run edit
         dbResult = getRealResult(resultsTable.getSchema(), realResultsTable.getName(), resultRowId);
-        assertTrue(dbResult.get("Created") == null && dbResult.get("Modified") == null);
+        assertTrue("Created and Modified in the provisioned result table weren't as expected", dbResult.get("Created") == null && dbResult.get("Modified") == null);
 
         // now edit the result
         QueryUpdateService resultsQUS = resultsTable.getUpdateService();
@@ -582,18 +584,18 @@
 
         // verify result created matches run's created in query table, but result modified now differs from run's created
         Map<String, Object> modifiedResults = new TableSelector(resultsTable, selectColumns, new SimpleFilter(runFieldKey, runRowId), null).getMap();
-        assertTrue(modifiedResults.get("Created").equals(runOriginalCreated));
-        assertFalse(modifiedResults.get("Created").equals(modifiedResults.get("Modified")));
-        assertFalse(modifiedResults.get("Modified").equals(runOriginalCreated));
-        assertFalse(modifiedResults.get("Modified").equals(runOriginalModified));
-        assertFalse(modifiedResults.get("Modified").equals(modifiedRunResults.get("Modified")));
+        assertEquals("modifiedResults Created didn't match runOriginalCreated", modifiedResults.get("Created"), runOriginalCreated);
+        assertNotEquals("modifiedResults Created shouldn't match modifiedResult Modified", modifiedResults.get("Created"), modifiedResults.get("Modified"));
+        assertNotEquals("modifiedResults Modified shouldn't match runOriginalCreated", modifiedResults.get("Modified"), runOriginalCreated);
+        assertNotEquals("modifiedResults Modified shouldn't match runOriginalModified", modifiedResults.get("Modified"), runOriginalModified);
+        assertNotEquals("modifiedResults Modified shouldn't match modifiedRunResults Modified", modifiedResults.get("Modified"), modifiedRunResults.get("Modified"));
 
         // verify modified in provisioned result table no longer null after result edit
         dbResult = getRealResult(resultsTable.getSchema(), realResultsTable.getName(), resultRowId);
-        assertTrue(dbResult.get("Created") == null && dbResult.get("CreatedBy") == null);
-        assertFalse(dbResult.get("Modified") == null || dbResult.get("ModifiedBy") == null);
-        assertTrue(dbResult.get("Modified").equals(modifiedResults.get("Modified")));
-        assertTrue(dbResult.get("ModifiedBy").equals(modifiedResults.get("ModifiedBy")));
+        assertTrue("dbResult shouldn't have Created or CreatedBy", dbResult.get("Created") == null && dbResult.get("CreatedBy") == null);
+        assertFalse("dbResult didn't have a Modified or ModifiedBy", dbResult.get("Modified") == null || dbResult.get("ModifiedBy") == null);
+        assertEquals("dbResults Modified didn't match", dbResult.get("Modified"), modifiedResults.get("Modified"));
+        assertEquals("dbResults ModifiedBy didn't match", dbResult.get("ModifiedBy"), modifiedResults.get("ModifiedBy"));
     }
 
     @Test

experiment/src/org/labkey/experiment/api/BaseFieldsTable.java

@@ -3,6 +3,7 @@
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.BaseColumnInfo;
+import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.JdbcType;
 import org.labkey.api.data.MutableColumnInfo;
@@ -13,6 +14,7 @@
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.FilteredTable;
 import org.labkey.api.security.permissions.AdminPermission;
+import org.labkey.api.security.permissions.Permission;
 
 public abstract class BaseFieldsTable extends FilteredTable<ExpSchema>
 {
@@ -32,6 +34,18 @@ public BaseFieldsTable(String tableName, @NotNull ExpSchema userSchema, @Nullabl
         addWrapColumn(_rootTable.getColumn("Description"));
         addWrapColumn(_rootTable.getColumn("RangeURI"));
         addWrapColumn(_rootTable.getColumn("StorageColumnName"));
+        addWrapColumn(_rootTable.getColumn("ConceptURI"));
+
+        // Add the other columns in case they're useful for future troubleshooting, but keep them out
+        // of the way by default
+        for (ColumnInfo column : _rootTable.getColumns())
+        {
+            if (getColumn(column.getName()) == null)
+            {
+                addWrapColumn(column).setHidden(true);
+            }
+        }
+
     }
 
     protected MutableColumnInfo addColumn(String name, JdbcType type)

experiment/src/org/labkey/experiment/api/PhiFieldsTable.java

@@ -18,8 +18,9 @@ public PhiFieldsTable(@NotNull ExpSchema userSchema, @Nullable ContainerFilter c
         setDescription("Shows one row for each PHI-annotated field in the selected folder(s). Rows are shown in " +
             "a folder or project only if the user has administrator permissions in that folder.");
 
-        MutableColumnInfo phi = addColumn("PHI", JdbcType.VARCHAR);
+        MutableColumnInfo phi = getMutableColumnOrThrow("PHI");
         phi.setDescription("PHI Annotation");
+        phi.setHidden(false);
 
         addCondition(new SimpleFilter(phi.getFieldKey(), "NotPHI", CompareType.NEQ));
     }