Changeset 6206

Timestamp:

Apr 12, 2021, 12:52:13 PM (13 months ago)

Author:

Nicklas Nordborg

Message:

References #1295: Registration of specimen handled by external lab

Implemented some checks that are displayed as warnings when importing. For example, if a date is in the future or older than 1 year.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/batch/import-external-specimen.js (modified) (1 diff)
• src/net/sf/basedb/reggie/plugins/cmd/DateValidator.java (modified) (5 diffs)
• src/net/sf/basedb/reggie/plugins/cmd/IntValidator.java (modified) (5 diffs)
• src/net/sf/basedb/reggie/plugins/cmd/LibraryInfo.java (modified) (1 diff)
• src/net/sf/basedb/reggie/plugins/cmd/LongValidator.java (modified) (4 diffs)
• src/net/sf/basedb/reggie/plugins/cmd/MergeInfo.java (modified) (1 diff)
• src/net/sf/basedb/reggie/plugins/cmd/PoolInfo.java (modified) (1 diff)
• src/net/sf/basedb/reggie/plugins/cmd/SequencingRunInfo.java (modified) (1 diff)

extensions/net.sf.basedb.reggie/trunk/resources/batch/import-external-specimen.js

@@ -99 +99 @@
       html += '</td>';
       html += '<td class="valid dottedleft">';
+      var startNo = 1;
       if (jsonFile && jsonFile.errors)
       {
-        html += '<div class="messagecontainer error"><ol>';
+        html += '<div class="messagecontainer error"><ol start="'+startNo+'">';
         for (var errNo = 0; errNo < jsonFile.errors.length; errNo++)
         {
           html += '<li>'+Strings.encodeTags(jsonFile.errors[errNo]);
         }
-        html += '</ol><div>';
-      }
-      else if (jsonFile && jsonFile.warnings)
-      {
-        html += '<div">'+Strings.encodeTags(jsonFile.warnings.join('<br>'))+'</div>';
+        html += '</ol></div>';
+        startNo += jsonFile.errors.length;
+      }
+      if (jsonFile && jsonFile.warnings)
+      {
+        html += '<div class="messagecontainer note"><ol start="'+startNo+'">';
+        for (var warnNo = 0; warnNo < jsonFile.warnings.length; warnNo++)
+        {
+          html += '<li>'+Strings.encodeTags(jsonFile.warnings[warnNo]);
+        }
+        html += '</ol></div>';
+        startNo += jsonFile.warnings.length;
       }
       html += '</td>';

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

@@ -6 +6 @@
 
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.reggie.Reggie;
 
 
@@ -15 +16 @@
 */
 public class DateValidator
-  implements ValueValidator<String, Date>
+  implements ValueValidator<String, Date>, Cloneable
 {
   /**
@@ -36 +37 @@
   private final DateFormat dateFormat;
   
+  private Date notAfter;
+  private Date notBefore;
+  
   public DateValidator(String format)
   {
@@ -42 +46 @@
   }
   
+  /**
+    Wrap this date validator with a validator that issue a warning
+    if the date is in the future.
+  */
+  public DateValidator warnIfFuture()
+  {
+    DateValidator wrap;
+    try 
+    {
+      wrap = (DateValidator)this.clone();
+      wrap.notAfter = new Date();
+    } 
+    catch (CloneNotSupportedException e) 
+    {
+      throw new UnsupportedOperationException("clone()");
+    }
+    return wrap;
+  }
+  
+  /**
+    Wrap this date validator with a validator that issue a warning
+    if the date is in the future or older than the specified number of
+    days.
+  */
+  public DateValidator warnIfFutureOrOlder(int numDays)
+  {
+    DateValidator wrap = warnIfFuture();
+    wrap.notBefore = new Date(wrap.notAfter.getTime()-numDays*86400l*1000l);
+    return wrap;
+  }
+  
+  /**
+    Wrap this date validator with a validator that issue a warning
+    if the date is in the future or older than the specified date.
+  */
+  public DateValidator warnIfFutureOrOlder(Date oldDate)
+  {
+    DateValidator wrap = warnIfFuture();
+    wrap.notBefore = oldDate;
+    return wrap;
+  }
+  
   @Override
   public Date isValid(DbControl dc, String value, JsonSection section, String entryKey) 
   {
+    Date result = null;
     try
     {
-      return dateFormat.parse(value);
+      result = dateFormat.parse(value);
     }
     catch (Exception ex)
@@ -53 +100 @@
       section.addErrorMessage("Invalid date in JSON: "+entryKey+"="+value+" (expected format: "+format+")");
     }
-    return null;
+    if (result != null)
+    {
+      if (notAfter != null && result.after(notAfter))
+      {
+        section.addWarningMessage("Future date in JSON: "+entryKey+"="+value);
+      }
+      if (notBefore != null && result.before(notBefore))
+      {
+        section.addWarningMessage("Old date in JSON: "+entryKey+"="+value+
+          " (expected after "+Reggie.CONVERTER_DATE_TO_STRING_WITH_SEPARATOR.format(notBefore)+")");
+      }
+    }
+    return result;
   }
   

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

@@ -12 +12 @@
 */
 public class IntValidator
-  implements ValueValidator<Object, Integer>
+  implements ValueValidator<Object, Integer>, Cloneable
 {
   /**
@@ -33 +33 @@
   private List<Integer> allowed;
   
+  private Integer softMax;
+  private Integer softMin;
+  
   /**
     Allow all integers.
@@ -42 +45 @@
     Allow all integers between min and max (inclusive).
     Null values are allowed and mean no limit.
+    Report either as error or warnings.
   */
   public IntValidator(Integer min, Integer max)
@@ -55 +59 @@
   {
     this.allowed = allowed;
+  }
+  
+  /**
+    Wrap this validator with a validator that create warnings
+    if the value is below the softMin or above the softMax limits.
+  */
+  public IntValidator warnIf(Integer softMin, Integer softMax)
+  {
+    IntValidator wrap;
+    try 
+    {
+      wrap = (IntValidator)this.clone();
+      wrap.softMax = softMax;
+      wrap.softMin = softMin;
+    } 
+    catch (CloneNotSupportedException e) 
+    {
+      throw new UnsupportedOperationException("clone()");
+    }
+    return wrap;
   }
   
@@ -97 +121 @@
       }
     }
+    if (result != null)
+    {
+      if (softMin != null && result < softMin)
+      {
+        section.addWarningMessage("Unexpected integer in JSON: "+entryKey+"="+value+" (expected >="+softMin+")");
+      }
+      if (softMax != null && result > softMax)
+      {
+        section.addWarningMessage("Unexpected integer in JSON: "+entryKey+"="+value+" (expected <="+softMax+")");
+      }
+    }
     return result;
   }

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

@@ -63 +63 @@
       }
       
-      libDate = section.getRequiredEntry("Date", DateValidator.YYYY_MM_DD);
-      libSize = section.getRequiredEntry("Library size", IntValidator.POSITIVE);
+      libDate = section.getRequiredEntry("Date", DateValidator.YYYY_MM_DD.warnIfFutureOrOlder(365));
+      libSize = section.getRequiredEntry("Library size", IntValidator.POSITIVE.warnIf(150, 400));
       libMolarity = section.getRequiredEntry("Library molarity", FloatValidator.POSITIVE);
       qubitConc = section.getRequiredEntry("Qubit concentration (ng/ul)", FloatValidator.POSITIVE);

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

@@ -11 +11 @@
 */
 public class LongValidator
-  implements ValueValidator<Object, Long>
+  implements ValueValidator<Object, Long>, Cloneable
 {
   /**
@@ -26 +26 @@
   private Long minValue;
   private List<Long> allowed;
+  private Long softMax;
+  private Long softMin;
   
   /**
@@ -50 +52 @@
     this.allowed = allowed;
   }
+  
+  /**
+    Wrap this validator with a validator that create warnings
+    if the value is below the softMin or above the softMax limits.
+  */
+  public LongValidator warnIf(Long softMin, Long softMax)
+  {
+    LongValidator wrap;
+    try 
+    {
+      wrap = (LongValidator)this.clone();
+      wrap.softMax = softMax;
+      wrap.softMin = softMin;
+    } 
+    catch (CloneNotSupportedException e) 
+    {
+      throw new UnsupportedOperationException("clone()");
+    }
+    return wrap;
+  }
+
   
   @Override
@@ -91 +114 @@
       }
     }
+    if (result != null)
+    {
+      if (softMin != null && result < softMin)
+      {
+        section.addWarningMessage("Unexpected long in JSON: "+entryKey+"="+value+" (expected >="+softMin+")");
+      }
+      if (softMax != null && result > softMax)
+      {
+        section.addWarningMessage("Unexpected long in JSON: "+entryKey+"="+value+" (expected <="+softMax+")");
+      }
+    }
     return result;
   }

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

@@ -20 +20 @@
     if (merge != null)
     {
-      pfReads = merge.getRequiredEntry("PF_READS", LongValidator.POSITIVE);
+      pfReads = merge.getRequiredEntry("PF_READS", LongValidator.POSITIVE.warnIf(10000000l, null)); // Warn if less than 10M reads
     }
     valid = merge != null && !merge.hasError();

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

@@ -46 +46 @@
         verifyUnusedBarcode(pool, libInfo.barcode, section);
       }
-      poolDate = section.getRequiredEntry("Date", DateValidator.YYYY_MM_DD);
+      poolDate = section.getRequiredEntry("Date", DateValidator.YYYY_MM_DD.warnIfFutureOrOlder(365));
       operator = section.getRequiredEntry("Operator");
     }

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

@@ -49 +49 @@
       position = section.getRequiredEntry("Position", PatternValidator.SEQUENCER_POSITION);
       runNumber = section.getRequiredEntry("RunNumber", IntValidator.POSITIVE);
-      startDate = section.getRequiredEntry("StartDate", DateValidator.YYMMDD);
-      endDate = section.getRequiredEntry("EndDate", DateValidator.YYMMDD_HH_MM_SS);
+      startDate = section.getRequiredEntry("StartDate", DateValidator.YYMMDD.warnIfFutureOrOlder(365));
+      endDate = section.getRequiredEntry("EndDate", DateValidator.YYMMDD_HH_MM_SS.warnIfFutureOrOlder(startDate));
       operator = section.getRequiredEntry("Operator");
       if (flowCellInfo.flowCell != null)