Changeset 1428

Timestamp:

Oct 31, 2011, 8:47:45 AM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #335: Use item subtypes - step 1

New items are now created with a subtype.

Location:

extensions/net.sf.basedb.reggie/branches/2.0-dev/src/net/sf/basedb/reggie

Files:

• dao/Patient.java (modified) (1 diff)
• servlet/ConsentFormServlet.java (modified) (2 diffs)
• servlet/PartitionRegistrationServlet.java (modified) (3 diffs)
• servlet/PersonalRegistrationServlet.java (modified) (3 diffs)
• servlet/SpecimenTubeServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/branches/2.0-dev/src/net/sf/basedb/reggie/dao/Patient.java

@@ -102 +102 @@
     loadAnnotations(dc, "gender", Reggie.ANNOTATION_GENDER, null);
     loadAnnotations(dc, "dateOfBirth", Reggie.ANNOTATION_DATE_OF_BIRTH, new DateToStringConverter(new SimpleDateFormat("yyyy-MM-dd")));
-    /*
-    // Date-of-birth need special handling for formatting
-    AnnotationType dateOfBirthType = Reggie.findAnnotationType(dc, Item.BIOSOURCE, Reggie.ANNOTATION_DATE_OF_BIRTH, true);
-    SimpleDateFormat df = new SimpleDateFormat("yyyy-MM-dd");
-    String dateOfBirth = df.format((Date)Reggie.getAnnotationValue(getBioSource(), dateOfBirthType));
-    setAnnotation("dateOfBirth", dateOfBirth);
-    */
-
   }
 

extensions/net.sf.basedb.reggie/branches/2.0-dev/src/net/sf/basedb/reggie/servlet/ConsentFormServlet.java

@@ -26 +26 @@
 import net.sf.basedb.reggie.dao.Case;
 import net.sf.basedb.reggie.dao.SpecimenTube;
+import net.sf.basedb.reggie.dao.Subtype;
 import net.sf.basedb.util.Values;
 import net.sf.basedb.util.error.ThrowableUtil;
@@ -162 +163 @@
           String caseName = (String)jsonCase.get("name");
           theCase = Sample.getNew(dc);
+          theCase.setItemSubtype(Subtype.CASE.load(dc));
           theCase.setName(caseName);
           if ("Not asked".equals(consent))

extensions/net.sf.basedb.reggie/branches/2.0-dev/src/net/sf/basedb/reggie/servlet/PartitionRegistrationServlet.java

@@ -28 +28 @@
 import net.sf.basedb.reggie.Reggie;
 import net.sf.basedb.reggie.converter.StringToDateConverter;
-import net.sf.basedb.reggie.dao.Case;
 import net.sf.basedb.reggie.dao.SpecimenTube;
+import net.sf.basedb.reggie.dao.Subtype;
 import net.sf.basedb.util.Values;
 import net.sf.basedb.util.error.ThrowableUtil;
@@ -160 +160 @@
               {
                 Extract lysExtract = specimen.newExtract(apWeight);
+                lysExtract.setItemSubtype(Subtype.LYSATE.load(dc));
                 lysExtract.setName(specimen.getName()+".l");
                 dc.saveItem(lysExtract);
@@ -201 +202 @@
               {
                 hisSample = Sample.getNew(dc);
+                hisSample.setItemSubtype(Subtype.HISTOLOGY.load(dc));
                 hisSample.setName(specimen.getName() + ".his");
                 dc.saveItem(hisSample);

extensions/net.sf.basedb.reggie/branches/2.0-dev/src/net/sf/basedb/reggie/servlet/PersonalRegistrationServlet.java

@@ -36 +36 @@
 import net.sf.basedb.reggie.dao.Patient;
 import net.sf.basedb.reggie.dao.SpecimenTube;
+import net.sf.basedb.reggie.dao.Subtype;
 import net.sf.basedb.util.MD5;
 import net.sf.basedb.util.Values;
@@ -276 +277 @@
           // Create new patient
           patient = BioSource.getNew(dc);
+          patient.setItemSubtype(Subtype.PATIENT.load(dc));
           patient.setName((String)jsonPat.get("name"));
           String pnr = (String)jsonPat.get("personalNumber");
@@ -329 +331 @@
           // Register a new case
           theCase = Sample.getNew(dc);
+          theCase.setItemSubtype(Subtype.CASE.load(dc));
           theCase.setName(originalCaseName);
           if (laterality != null)

extensions/net.sf.basedb.reggie/branches/2.0-dev/src/net/sf/basedb/reggie/servlet/SpecimenTubeServlet.java

@@ -29 +29 @@
 import net.sf.basedb.reggie.dao.Case;
 import net.sf.basedb.reggie.dao.SpecimenTube;
+import net.sf.basedb.reggie.dao.Subtype;
 import net.sf.basedb.util.Values;
 import net.sf.basedb.util.error.ThrowableUtil;
@@ -264 +265 @@
             JSONObject jsonSpec = (JSONObject)jsonSpecimen.get(i);
             Sample specimen = Sample.getNew(dc);
+            specimen.setItemSubtype(Subtype.SPECIMEN.load(dc));
             specimen.setName((String)jsonSpec.get("name"));
             dc.saveItem(specimen);