Changeset 5757

Timestamp:

Nov 26, 2019, 9:25:39 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1206: The MIPs aliquot importer should handle some values as special cases

Implemented the NormalTumor and Variant translations.

File:

• extensions/net.sf.basedb.reggie/branches/4.24-stable/src/net/sf/basedb/reggie/plugins/AliquotImporter.java (modified) (4 diffs)

extensions/net.sf.basedb.reggie/branches/4.24-stable/src/net/sf/basedb/reggie/plugins/AliquotImporter.java

@@ -23 +23 @@
 import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.reggie.Reggie;
+import net.sf.basedb.reggie.converter.ValueConverter;
 import net.sf.basedb.reggie.dao.Annotationtype;
 import net.sf.basedb.reggie.dao.BioplateType;
@@ -190 +191 @@
     Mapper patientIdMapper = getOptionalMapper(ffp, "PatientID", fileAndLine);
     Mapper provnummerMapper = getOptionalMapper(ffp, "Provnummer", fileAndLine);
+    
+    ValueConverter<String, String> normalTumorConverter = new TranslationConverter("TUMOR", "T", "NA", null);
+    ValueConverter<String, String> variantConverter = new TranslationConverter("0", null);
     
     while (ffp.hasMoreData())
@@ -211 +215 @@
       a.poolVolume = poolVolumeMapper.getString(data);
       if (commentMapper != null) a.comment = commentMapper.getString(data);
-      if (normalTumorMapper != null) a.normalTumor = normalTumorMapper.getString(data);
+      if (normalTumorMapper != null) a.normalTumor = normalTumorConverter.convert(normalTumorMapper.getString(data));
       if (formMapper != null) a.form = formMapper.getString(data);
-      if (variantMapper != null) a.variant = variantMapper.getString(data);
+      if (variantMapper != null) a.variant = variantConverter.convert(variantMapper.getString(data));
       if (variantListMapper != null) a.variantList = variantListMapper.getString(data);
       if (screeningMapper != null) a.screening = screeningMapper.getString(data);
@@ -664 +668 @@
     
   }
+  
+  /**
+    A simple converter for string values. If a value is found in the 
+    translation map the translation is returned. Otherwise the original
+    value is returned unmodified.
+  */
+  public static class TranslationConverter
+    implements ValueConverter<String, String>
+  {
+
+    private final Map<String, String> translation;
+    
+    /**
+      Create a new translation. Key and values are provided
+      as a single array with pair-wise entries. Eg.
+      mapping[0] translates to mapping[1], mapping[2] translates to 
+      mapping[3], and so on.
+    */
+    public TranslationConverter(String... mapping) 
+    {
+      this.translation = new HashMap<>();
+      for (int i = 1; i < mapping.length; i+=2)
+      {
+        translation.put(mapping[i-1], mapping[i]);
+      }
+    }
+    
+    @Override
+    public String convert(String key) 
+    {
+      return translation.containsKey(key) ? translation.get(key) : key;
+    }
+  }
 }