Changeset 5781

Timestamp:

Dec 11, 2019, 12:34:23 PM (2 years ago)

Author:

Nicklas Nordborg

Message:

References #1209: Add support for storing TMA specimen

Added support for using either "Name" or "External ID" to reference existing cases.

File:

• extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/TMASpecimenImporter.java (modified) (12 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/TMASpecimenImporter.java

@@ -22 +22 @@
 import net.sf.basedb.core.Sample;
 import net.sf.basedb.core.StringParameterType;
-import net.sf.basedb.core.Type;
 import net.sf.basedb.core.plugin.GuiContext;
 import net.sf.basedb.core.plugin.InteractivePlugin;
@@ -29 +28 @@
 import net.sf.basedb.core.plugin.Request;
 import net.sf.basedb.core.plugin.Response;
-import net.sf.basedb.core.query.Expressions;
-import net.sf.basedb.core.query.Hql;
-import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.plugins.AbstractFlatFileImporter;
+import net.sf.basedb.plugins.batchimport.IdMethod;
+import net.sf.basedb.plugins.batchimport.PropertyIdMethod;
 import net.sf.basedb.plugins.util.Parameters;
 import net.sf.basedb.reggie.Reggie;
@@ -39 +37 @@
 import net.sf.basedb.reggie.dao.ReggieItem;
 import net.sf.basedb.reggie.dao.Subtype;
+import net.sf.basedb.util.Enumeration;
 import net.sf.basedb.util.parser.ConfigureByExample;
 import net.sf.basedb.util.parser.FlatFileParser;
@@ -65 +64 @@
   private static final PluginParameter<String> caseColumnMapping = new PluginParameter<String>(
       "caseColumnMapping",
-      "Case",
-      "Mapping that picks the name of the Case from the data columns. This " +
+      "Case ID",
+      "Mapping that picks the name or external id for the Case from the data columns. This " +
       "parameter is required. " +
-      "Example: \\Case\\",
+      "Example: \\Case ID\\",
       requiredColumnMapping
       );
@@ -156 +155 @@
   // ------------------------------------
 
+  protected IdMethod[] getIdMethods()
+  {
+    return new IdMethod[] { PropertyIdMethod.NAME, PropertyIdMethod.EXTERNAL_ID };
+  }
+  
+  /**
+    Get the id method to use for finding cases. This implementation 
+    searches the methods returned by {@link #getIdMethods()} 
+  */
+  protected IdMethod getIdMethod(String method)
+  {
+    for (IdMethod im : getIdMethods())
+    {
+      if (im.getMethod().equals(method))
+      {
+        return im;
+      }
+    }
+    return PropertyIdMethod.NAME;
+  }
+  
   @Override
   public RequestInformation getRequestInformation(GuiContext context, String command) 
@@ -199 +219 @@
           return;
         }
+        
+        // Check that a mapping has been provided for the selected idMethod
+        IdMethod idMethod = getIdMethod((String)request.getParameterValue("idMethod"));
+        if (idMethod == null)
+        {
+          response.setError("Unknown method for item identification: " + 
+              request.getParameterValue("idMethod"), null);
+          return;
+        }
 
         // Check the mapping expressions
@@ -208 +237 @@
         storeValue(wrapper, request, ri.getParameter(Parameters.LOGFILE_PARAMETER));
         storeValue(wrapper, request, excelSheetParameter);
+        storeValue(wrapper, request, ri.getParameter("idMethod"));
 
         storeValue(wrapper, request, dataHeaderRegexpParameter);
@@ -245 +275 @@
   private DbControl dc;
   private FlatFileParser ffp;
+  private IdMethod idMethod;
   private ItemQuery<Sample> caseQuery;
   private Mapper caseMapper;
@@ -262 +293 @@
     this.dc = sc.newDbControl();
     this.dryRun = job.getJob().isDryRun();
+    this.idMethod = getIdMethod(job.getValue("idMethod"));
     this.caseQuery = Sample.getQuery();
     Subtype.CASE.addFilter(dc, caseQuery);
     caseQuery.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
-    caseQuery.restrict(Restrictions.eq(Hql.property("name"), Expressions.parameter("caseName")));
+    idMethod.prepareQuery(dc, caseQuery);
     if (ffp.getExcelSheet() != null)
     {
@@ -275 +307 @@
   protected void beginData()
   {
-    caseMapper = NotNullMapper.wrap("Case name is null", getMapper(ffp, job.getValue("caseColumnMapping"), null, null));
+    caseMapper = NotNullMapper.wrap("Case ID is null", getMapper(ffp, job.getValue("caseColumnMapping"), null, null));
     tmaBlockMapper = NotNullMapper.wrap("TMABlock is null", getMapper(ffp, job.getValue("tmaBlockColumnMapping"), null, null));
     tmaBlockPosMapper = NotNullMapper.wrap("TMABlockPos is null", getMapper(ffp, job.getValue("tmaBlockPosColumnMapping"), null, null));
@@ -287 +319 @@
     throws BaseException
   {
-    String caseName = caseMapper.getString(data);
-    caseQuery.setParameter("caseName", caseName, Type.STRING);
-    List<Sample> cases = caseQuery.list(dc);
+    String caseId = caseMapper.getString(data);
+    List<Sample> cases = idMethod.find(dc, caseQuery, caseId);
     if (cases.size() > 1)
     {
-      throw new InvalidDataException("Found " + cases.size() + " cases with the same name (" + caseName + ").");
+      throw new InvalidDataException("Found " + cases.size() + " cases [" + idMethod + "=" + caseId + "]");
     }
     else if (cases.size() == 0)
     {
-      throw new ItemNotFoundException("Case[name=" + caseName + "]");
+      throw new ItemNotFoundException("Case[" + idMethod + "=" + caseId + "]");
     }
 
@@ -380 +411 @@
         parameters.add(Parameters.dryRunParameter(null, null, null));
         
+        Enumeration<String, String> idMethods = new Enumeration<String, String>();
+        idMethods.add(null, null);
+        idMethods.add(PropertyIdMethod.NAME.getMethod(), PropertyIdMethod.NAME.getTitle());
+        idMethods.add(PropertyIdMethod.EXTERNAL_ID.getMethod(), PropertyIdMethod.EXTERNAL_ID.getTitle());
+        PluginParameter<String> idMethodParameter = new PluginParameter<String>(
+          "idMethod",
+          "Case identification method",
+          "The method to use for finding existing cases. The plug-in can use either the " +
+          "SCAN-B ID or the Release ID.",
+          new StringParameterType(null, null, true, 1, 0, 0, idMethods)
+        );
+        parameters.add(idMethodParameter);
+
+        
         // Parser regular expressions
         parameters.add(parserSection);