nmdp-bioinformatics · heuermh · Nov 1, 2017
diff --git a/hml/HEADER.txt b/hml/HEADER.txt
@@ -1,7 +1,7 @@
 /*
 
     ngs-hml  Mapping for HML XSDs.
-    Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
+    Copyright (c) 2014-2017 National Marrow Donor Program (NMDP)
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published

diff --git a/hml/pom.xml b/hml/pom.xml
@@ -2,7 +2,7 @@
 <!--
 
     ngs-hml  Mapping for HML XSDs.
-    Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
+    Copyright (c) 2014-2017 National Marrow Donor Program (NMDP)
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -89,8 +89,8 @@
             <configuration>
               <xsdOptions>
                 <xsdOption>
-                  <xsd>src/main/xsd/hml-1.0.1.xsd</xsd>
-                  <bindingFile>src/main/xsd/hml-1.0.1.xjb</bindingFile>
+                  <xsd>src/main/xsd/hml-1.0.2.xsd</xsd>
+                  <bindingFile>src/main/xsd/hml-1.0.2.xjb</bindingFile>
                   <extension>true</extension>
                 </xsdOption>
               </xsdOptions>

diff --git a/hml/src/main/java/org/nmdp/ngs/hml/HmlReader.java b/hml/src/main/java/org/nmdp/ngs/hml/HmlReader.java
@@ -1,7 +1,7 @@
 /*
 
     ngs-hml  Mapping for HML XSDs.
-    Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
+    Copyright (c) 2014-2017 National Marrow Donor Program (NMDP)
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -77,7 +77,7 @@ public static Hml read(final Reader reader) throws IOException {
             JAXBContext context = JAXBContext.newInstance(Hml.class);
             Unmarshaller unmarshaller = context.createUnmarshaller();
             SchemaFactory schemaFactory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
-            URL schemaURL = HmlReader.class.getResource("/org/nmdp/ngs/hml/xsd/hml-1.0.1.xsd");
+            URL schemaURL = HmlReader.class.getResource("/org/nmdp/ngs/hml/xsd/hml-1.0.2.xsd");
             Schema schema = schemaFactory.newSchema(schemaURL);
             unmarshaller.setSchema(schema);
             return (Hml) unmarshaller.unmarshal(reader);

diff --git a/hml/src/main/java/org/nmdp/ngs/hml/HmlUtils.java b/hml/src/main/java/org/nmdp/ngs/hml/HmlUtils.java
@@ -1,7 +1,7 @@
 /*
 
     ngs-hml  Mapping for HML XSDs.
-    Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
+    Copyright (c) 2014-2017 National Marrow Donor Program (NMDP)
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published

diff --git a/hml/src/main/java/org/nmdp/ngs/hml/HmlValidationException.java b/hml/src/main/java/org/nmdp/ngs/hml/HmlValidationException.java
@@ -1,7 +1,7 @@
 /*
 
     ngs-hml  Mapping for HML XSDs.
-    Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
+    Copyright (c) 2014-2017 National Marrow Donor Program (NMDP)
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published

diff --git a/hml/src/main/java/org/nmdp/ngs/hml/HmlValidationRule.java b/hml/src/main/java/org/nmdp/ngs/hml/HmlValidationRule.java
@@ -1,7 +1,7 @@
 /*
 
     ngs-hml  Mapping for HML XSDs.
-    Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
+    Copyright (c) 2014-2017 National Marrow Donor Program (NMDP)
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published

diff --git a/hml/src/main/java/org/nmdp/ngs/hml/HmlValidator.java b/hml/src/main/java/org/nmdp/ngs/hml/HmlValidator.java
@@ -1,7 +1,7 @@
 /*
 
     ngs-hml  Mapping for HML XSDs.
-    Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
+    Copyright (c) 2014-2017 National Marrow Donor Program (NMDP)
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published

diff --git a/hml/src/main/java/org/nmdp/ngs/hml/HmlWriter.java b/hml/src/main/java/org/nmdp/ngs/hml/HmlWriter.java
@@ -1,7 +1,7 @@
 /*
 
     ngs-hml  Mapping for HML XSDs.
-    Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
+    Copyright (c) 2014-2017 National Marrow Donor Program (NMDP)
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -75,7 +75,7 @@ public static void write(final Hml data, final Writer writer) throws IOException
             JAXBContext context = JAXBContext.newInstance(Hml.class);
             Marshaller marshaller = context.createMarshaller();
             SchemaFactory schemaFactory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);
-            URL schemaURL = HmlReader.class.getResource("/org/nmdp/ngs/hml/xsd/hml-1.0.1.xsd");
+            URL schemaURL = HmlReader.class.getResource("/org/nmdp/ngs/hml/xsd/hml-1.0.2.xsd");
             Schema schema = schemaFactory.newSchema(schemaURL);
             marshaller.setSchema(schema);
             marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);

diff --git a/hml/src/main/java/org/nmdp/ngs/hml/jaxb/package-info.java b/hml/src/main/java/org/nmdp/ngs/hml/jaxb/package-info.java
@@ -1,7 +1,7 @@
 /*
 
     ngs-hml  Mapping for HML XSDs.
-    Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
+    Copyright (c) 2014-2017 National Marrow Donor Program (NMDP)
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published

diff --git a/hml/src/main/java/org/nmdp/ngs/hml/package-info.java b/hml/src/main/java/org/nmdp/ngs/hml/package-info.java
@@ -1,7 +1,7 @@
 /*
 
     ngs-hml  Mapping for HML XSDs.
-    Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
+    Copyright (c) 2014-2017 National Marrow Donor Program (NMDP)
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published

diff --git a/hml/src/main/java/org/nmdp/ngs/hml/rules/AbstractHmlValidationRule.java b/hml/src/main/java/org/nmdp/ngs/hml/rules/AbstractHmlValidationRule.java
@@ -1,7 +1,7 @@
 /*
 
     ngs-hml  Mapping for HML XSDs.
-    Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
+    Copyright (c) 2014-2017 National Marrow Donor Program (NMDP)
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published

diff --git a/hml/src/main/java/org/nmdp/ngs/hml/rules/HmlValidationRules.java b/hml/src/main/java/org/nmdp/ngs/hml/rules/HmlValidationRules.java
@@ -1,7 +1,7 @@
 /*
 
     ngs-hml  Mapping for HML XSDs.
-    Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
+    Copyright (c) 2014-2017 National Marrow Donor Program (NMDP)
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published

diff --git a/hml/src/main/java/org/nmdp/ngs/hml/rules/HmlValidatorImpl.java b/hml/src/main/java/org/nmdp/ngs/hml/rules/HmlValidatorImpl.java
@@ -1,7 +1,7 @@
 /*
 
     ngs-hml  Mapping for HML XSDs.
-    Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
+    Copyright (c) 2014-2017 National Marrow Donor Program (NMDP)
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published

diff --git a/hml/src/main/java/org/nmdp/ngs/hml/rules/MiringModule.java b/hml/src/main/java/org/nmdp/ngs/hml/rules/MiringModule.java
@@ -1,7 +1,7 @@
 /*
 
     ngs-hml  Mapping for HML XSDs.
-    Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
+    Copyright (c) 2014-2017 National Marrow Donor Program (NMDP)
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published

diff --git a/hml/src/main/java/org/nmdp/ngs/hml/rules/package-info.java b/hml/src/main/java/org/nmdp/ngs/hml/rules/package-info.java
@@ -1,7 +1,7 @@
 /*
 
     ngs-hml  Mapping for HML XSDs.
-    Copyright (c) 2014-2015 National Marrow Donor Program (NMDP)
+    Copyright (c) 2014-2017 National Marrow Donor Program (NMDP)
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published

diff --git a/...ources/org/nmdp/ngs/hml/xsd/hml-1.0.1.xsd → ...ources/org/nmdp/ngs/hml/xsd/hml-1.0.2.xsd b/...ources/org/nmdp/ngs/hml/xsd/hml-1.0.1.xsd → ...ources/org/nmdp/ngs/hml/xsd/hml-1.0.2.xsd
@@ -22,12 +22,12 @@
 
 -->
 <xs:schema 
-  xmlns="http://schemas.nmdp.org/spec/hml/1.0.1"
-  xmlns:hmlns="http://schemas.nmdp.org/spec/hml/1.0.1" 
+  xmlns="http://schemas.nmdp.org/spec/hml/1.0"
+  xmlns:hmlns="http://schemas.nmdp.org/spec/hml/1.0" 
   xmlns:xs="http://www.w3.org/2001/XMLSchema" 
   elementFormDefault="qualified" attributeFormDefault="unqualified" 
-  targetNamespace="http://schemas.nmdp.org/spec/hml/1.0.1"
-  version="1.0.1">
+  targetNamespace="http://schemas.nmdp.org/spec/hml/1.0"
+  version="1.0.2">
 
   <!-- HML document root -->
   <xs:element name="hml" id="hml" nillable="false">
@@ -59,7 +59,8 @@
       </xs:sequence>
       <xs:attribute name="version" use="required">
         <xs:annotation><xs:documentation>
-          Expected to be '1.0.1' to use this version of the HML schema.
+          Expected to be a '1.0.x' version like '1.0.2' to use this version of the HML schema.
+          HML 1.0.2 released March 2016.
         </xs:documentation></xs:annotation>
         <xs:simpleType id="version">
           <xs:restriction base="xs:string">
@@ -79,42 +80,6 @@
   </xs:element>
 
 
-  <!-- REPORTING-CENTER -->
-  <xs:element name="reporting-center" id="reporting-center">
-    <xs:annotation><xs:documentation>
-        This element identifies the entity/organization sending this HML data. 
-        If included, must contain a unique ID identifying the sender as well as 
-        a context which defines to whom the ID is meaningful or the source 
-        of the ID.
-        This element is required for NMDP transactions and if context is not 
-        included, is assumed to be "NMDP".
-
-        Attributes:
-        -----------
-        - reporting-center-id:      (required) Unique id of reporting center 
-                                    like "789".
-        - reporting-center-context: (optional) Source of the reporting center ID 
-                                    like "NMDP".  To whom the ID is meaningful.
-    </xs:documentation></xs:annotation>
-    <xs:complexType>
-      <xs:attribute name="reporting-center-id" use="required" >
-        <xs:simpleType>
-          <xs:restriction base="xs:string" >
-            <xs:minLength value="1" />
-          </xs:restriction>
-        </xs:simpleType>
-      </xs:attribute>      
-      <xs:attribute name="reporting-center-context" use="optional" default="NMDP">
-        <xs:simpleType>
-          <xs:restriction base="xs:string" >
-            <xs:minLength value="1" />
-          </xs:restriction>
-        </xs:simpleType>
-      </xs:attribute>
-    </xs:complexType>
-  </xs:element>
-
-
   <!-- HMLID -->
   <xs:complexType name="hmlid">
     <xs:annotation><xs:documentation>
@@ -132,9 +97,16 @@
         -----------
          - root:        Unique publicly registered identifier for the HML 
                         creator's organization.  
-                        (ex: NMDP HL7 id is "2.16.840.1.113883.3.1470")
-                        Format is expected to be a string of digits and dot 
-                        delimiters.  (required)
+                        Examples: 
+
+                          HL7: NMDP HL7 id is "2.16.840.1.113883.3.1470"
+                          <hmlid root="2.16.840.1.113883.3.1470" extension="20160316-testrun001" />
+
+                          UUID:
+                          <hmlid root="b044f879-f10b-4942-b8e6-e00e42d57fbe" />
+
+                        Root format is expected to be a string of digits with 
+                        dot or dash delimiters.  (required)
          - extension:   A unique document identifier managed internally by the 
                         organization specified in 'root'. Can be any alpha-numeric 
                         format desired by the organization. (ex: "hml-0.9.7-123456789.23a")
@@ -154,10 +126,11 @@
     <xs:annotation><xs:documentation>
       Unique publicly registered identifier for the HML creator's organization.  
       This can be an HL7 compliant field (ex: NMDP is "2.16.840.1.113883.3.1470")
-      Format is expected to be a string of digits and dot delimiters. (required)
+      The format can also be a UUID like "5177ec14-495b-4fea-a8fc-de1311f241cd".
+      Format is expected to be a string of digits and dot or hyphen delimiters. (required)
     </xs:documentation></xs:annotation>
     <xs:restriction base="xs:string">
-      <xs:pattern value="([0-9\.])+" />    
+      <xs:pattern value="([0-9a-zA-Z\.\-])+" />    
     </xs:restriction>
   </xs:simpleType>
 
@@ -177,6 +150,42 @@
   </xs:simpleType>
 
 
+  <!-- REPORTING-CENTER -->
+  <xs:element name="reporting-center" id="reporting-center">
+    <xs:annotation><xs:documentation>
+        This element identifies the entity/organization sending this HML data. 
+        If included, must contain a unique ID identifying the sender as well as 
+        a context which defines to whom the ID is meaningful or the source 
+        of the ID.
+        This element is required for NMDP transactions and if context is not 
+        included, is assumed to be "NMDP".
+
+        Attributes:
+        -----------
+        - reporting-center-id:      (required) Unique id of reporting center 
+                                    like "789".
+        - reporting-center-context: (optional) Source of the reporting center ID 
+                                    like "NMDP".  To whom the ID is meaningful.
+    </xs:documentation></xs:annotation>
+    <xs:complexType>
+      <xs:attribute name="reporting-center-id" use="required" >
+        <xs:simpleType>
+          <xs:restriction base="xs:string" >
+            <xs:minLength value="1" />
+          </xs:restriction>
+        </xs:simpleType>
+      </xs:attribute>      
+      <xs:attribute name="reporting-center-context" use="optional" default="NMDP">
+        <xs:simpleType>
+          <xs:restriction base="xs:string" >
+            <xs:minLength value="1" />
+          </xs:restriction>
+        </xs:simpleType>
+      </xs:attribute>
+    </xs:complexType>
+  </xs:element>
+
+
   <!-- TYPING-TEST-NAMES -->
   <xs:complexType name="typing-test-names">
     <xs:annotation><xs:documentation>
@@ -245,7 +254,7 @@
     </xs:documentation></xs:annotation>
     <xs:sequence>
       <!-- Extensible letting a property have special-use child elements -->
-      <xs:any minOccurs="0" maxOccurs="unbounded" />
+      <xs:any namespace="##any" processContents="lax" minOccurs="0" maxOccurs="unbounded" />
     </xs:sequence>    
     <xs:attribute name="name" use="required">
       <xs:simpleType>
@@ -754,7 +763,7 @@
 
         Children:
         ---------
-        - amplification     (required, qty: 1)
+        - amplification     (not required, qty: 0 or 1)
         - sub-amplification (not required, qty: 0 or more)
         - gssp              (not required, qty: 0 or more)
 
@@ -783,7 +792,7 @@
     </xs:documentation></xs:annotation>
     <xs:sequence>
       <xs:element name="property"          type="hmlns:property" minOccurs="0" maxOccurs="unbounded" />
-      <xs:element name="amplification"     type="hmlns:amplification" minOccurs="1" maxOccurs="1" />
+      <xs:element name="amplification"     type="hmlns:amplification" minOccurs="0" maxOccurs="1" />
       <xs:element name="sub-amplification" type="hmlns:sub-amplification" minOccurs="0" maxOccurs="unbounded" />
       <xs:element name="gssp"              type="hmlns:gssp" minOccurs="0" maxOccurs="unbounded" />
     </xs:sequence>
@@ -833,9 +842,7 @@
       <xs:restriction base="hmlns:sequence">
         <xs:attribute name="registered-name" use="required">
           <xs:simpleType>
-            <xs:restriction base="xs:string">
-              <xs:minLength value="1" />
-            </xs:restriction>
+            <xs:restriction base="xs:string"></xs:restriction>
           </xs:simpleType>
         </xs:attribute>
       </xs:restriction>
@@ -1313,7 +1320,7 @@
             <!-- 
             Genome Reference Consortium:
               <reference-database ... >
-                  <reference-sequence id="1"
+                  <reference-sequence id="ref1"
                                   name="HSCHR6_MHC_MCF_CTG1" 
                                   start="0"
                                   end="4827813"
@@ -1324,7 +1331,7 @@
 
             IMGT/HLA:
               <reference-database ... >
-                  <reference-sequence id="3"
+                  <reference-sequence id="ref3"
                                   name="HLA-A*01:01:01:01"
                                   start="0"
                                   end="3053"
@@ -1335,7 +1342,7 @@
 
             No database reference:
               <reference-database availability="none">
-                  <reference-sequence id="0"/>
+                  <reference-sequence id="ref0"/>
               </reference-database>
             -->
 
@@ -1564,8 +1571,8 @@
         - paired: true/false (default) (required)
         - pooled: true/false (default) (required)
         - availability: public|private|permission (optional)
-        - adapterTrimmed: true/false (default) (required)
-        - qualityTrimmed: true/false (default) (required)
+        - adapter-trimmed: true/false (default) (required)
+        - quality-trimmed: true/false (default) (required)
     </xs:documentation></xs:annotation>
     <xs:attribute name="uri" use="required">
       <xs:simpleType>