Changeset 6457

Timestamp:

Nov 1, 2021, 8:58:28 AM (15 months ago)

Author:

Nicklas Nordborg

Message:

References #1347: Updates to registration of specimen handled by external lab

Implemented support for checking FASTQ file size.

Location:

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/cmd

Files:

• FastqInfo.java (modified) (4 diffs)
• JsonSection.java (modified) (1 diff)
• LongValidator.java (modified) (4 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/cmd/FastqInfo.java

@@ -34 +34 @@
       R1 = fastq.getRequiredEntry("R1", new FastqFile());
       R2 = fastq.getRequiredEntry("R2", new FastqFile());
-      // TODO -- wait and see
-      if (R1 != null) R1.md5 = fastq.getOptionalEntry("R1 MD5", PatternValidator.MD5);
-      if (R2 != null) R2.md5 = fastq.getOptionalEntry("R2 MD5", PatternValidator.MD5);
+      if (R1 != null) 
+      {
+        //R1.md5 = fastq.getOptionalEntry("R1 MD5", PatternValidator.MD5);
+        R1.expectedSize = fastq.getOptionalEntry("R11size", LongValidator.POSITIVE_OR_NULL);
+      }
+      if (R2 != null) 
+      {
+        //R2.md5 = fastq.getOptionalEntry("R2 MD5", PatternValidator.MD5);
+        R2.expectedSize = fastq.getOptionalEntry("R2size", LongValidator.POSITIVE_OR_NULL);
+      }
     }
     valid = fastq != null && !fastq.hasError();
@@ -55 +62 @@
       FileMetaData info = new FileMetaData();
       tmp = session.readFile(directory+f.name, info);
-      f.size = info.getSize();
+      f.actualSize = info.getSize();
       f.lastModified = info.getLastModifiedTime();
-      if (f.size == 0)
+      if (f.actualSize == 0)
       {
         section.addErrorMessage("FASTQ file is missing: " + f.name);
+      }
+      else if (f.expectedSize != null && f.actualSize != f.expectedSize)
+      {
+        section.addErrorMessage("FASTQ file size: "+f.name+"="+f.actualSize+" (expected "+f.expectedSize+" bytes)");
       }
     }
@@ -78 +89 @@
     public String name;
     public String md5;
-    public long size;
+    public Long expectedSize;
+    public long actualSize;
     public long lastModified;
     
@@ -102 +114 @@
       j.put("name", name);
       j.put("md5", md5);
-      j.put("size", size);
+      j.put("size", actualSize);
       j.put("lastModified", Reggie.CONVERTER_DATETIME_TO_STRING_WITH_SEPARATOR.convert(new Date(lastModified)));
       return j;

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/cmd/JsonSection.java

@@ -89 +89 @@
     Get an optional entry from the JSON file. A validator is
     optional, but if a validator is given it will be called
-    also for null values.
+    also for null values (but not if the entry is missing).
   */
   @SuppressWarnings("unchecked")
   public <T, F> T getOptionalEntry(String key, ValueValidator<F, T> validator)
   {
-    Object val = json.get(key);
     T result = null;
-    if (validator != null)
+    if (json.containsKey(key))
     {
-      if (val != null && !validator.getExpectedClass().isInstance(val))
+      Object val = json.get(key);
+      if (validator != null)
       {
-        addErrorMessage("Invalid entry in JSON: "+section+"."+key+"="+val+
-          " (expected "+validator.getExpectedClass().getSimpleName()+", got " + val.getClass().getSimpleName()+")");
+        if (val != null && !validator.getExpectedClass().isInstance(val))
+        {
+          addErrorMessage("Invalid entry in JSON: "+section+"."+key+"="+val+
+            " (expected "+validator.getExpectedClass().getSimpleName()+", got " + val.getClass().getSimpleName()+")");
+        }
+        else
+        {
+          try
+          {
+            result = validator.isValid(file.dc(), (F)val, this, section+"."+key);
+          }
+          catch (Exception ex)
+          {
+            addErrorMessage("Invalid entry in JSON: "+section+"."+key+"="+val+" ("+ex.getMessage()+")");
+          }
+        }
       }
       else
       {
-        try
-        {
-          result = validator.isValid(file.dc(), (F)val, this, section+"."+key);
-        }
-        catch (Exception ex)
-        {
-          addErrorMessage("Invalid entry in JSON: "+section+"."+key+"="+val+" ("+ex.getMessage()+")");
-        }
+        result = (T)val;
       }
-    }
-    else
-    {
-      result = (T)val;
     }
     return result;

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/cmd/LongValidator.java

@@ -16 +16 @@
     Allow all long values.
   */
-  public static final LongValidator ALL = new LongValidator();
+  public static final LongValidator ALL = new LongValidator(false);
+  
+  /**
+    All all long and null values.
+    @since 4.33.4
+  */
+  public static final LongValidator ALL_OR_NULL = new LongValidator(true);
   
   /**
     All positive values > 0.
   */
-  public static final LongValidator POSITIVE = new LongValidator(1l, null);
+  public static final LongValidator POSITIVE = new LongValidator(1l, null, false);
+
+  /**
+    All positive values > 0 or null.
+    @since 4.33.4
+  */
+  public static final LongValidator POSITIVE_OR_NULL = new LongValidator(1l, null, true);
   
+  private boolean allowNull;
   private Long maxValue;
   private Long minValue;
@@ -30 +43 @@
   
   /**
-    Allow all integers.
+    Allow all long values.
   */
-  public LongValidator() 
-  {}
+  public LongValidator(boolean allowNull) 
+  {
+    this.allowNull = allowNull;
+  }
   
   /**
@@ -39 +54 @@
     Null values are allowed and mean no limit.
   */
-  public LongValidator(Long min, Long max)
+  public LongValidator(Long min, Long max, boolean allowNull)
   {
     this.minValue = min;
     this.maxValue = max;
+    this.allowNull = allowNull;
   }
   
@@ -84 +100 @@
   {
     Long result = null;
-    if (value instanceof Number)
+    if (value == null)
+    {
+      if (!allowNull)
+      {
+        section.addErrorMessage("Missing long in JSON: "+entryKey);
+      }
+    }
+    else if (value instanceof Number)
     {
       result = ((Number)value).longValue();