rework OID handling for better OID -> CodeSystem resolution

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/IWorkerContext.java

@@ -4,6 +4,7 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.Collection;
 import java.util.Date;
+import java.util.HashSet;
 
 /*
   Copyright (c) 2011+, HL7, Inc.
@@ -45,6 +46,7 @@ import org.fhir.ucum.UcumService;
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.TerminologyServiceException;
+import org.hl7.fhir.r5.context.IWorkerContext.OIDDefinition;
 import org.hl7.fhir.r5.elementmodel.Element;
 import org.hl7.fhir.r5.formats.IParser;
 import org.hl7.fhir.r5.formats.ParserType;
@@ -70,6 +72,7 @@ import org.hl7.fhir.r5.terminologies.utilities.CodingValidationRequest;
 import org.hl7.fhir.r5.terminologies.utilities.ValidationResult;
 import org.hl7.fhir.r5.utils.validation.IResourceValidator;
 import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier;
+import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
 import org.hl7.fhir.utilities.FhirPublication;
 import org.hl7.fhir.utilities.TimeTracker;
 import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
@@ -102,6 +105,93 @@ import javax.annotation.Nonnull;
 
 public interface IWorkerContext {
 
+  public class OIDDefinition {
+    private String type;
+    private String oid;
+    private String url;
+    private String version;
+    private String packageSrc;
+    protected OIDDefinition(String type, String oid, String url, String version, String packageSrc) {
+      super();
+      this.type = type;
+      this.oid = oid;
+      this.url = url;
+      this.version = version;
+      this.packageSrc = packageSrc;
+    }
+    public String getType() {
+      return type;
+    }
+    public String getOid() {
+      return oid;
+    }
+    public String getUrl() {
+      return url;
+    }
+    public String getVersion() {
+      return version;
+    }
+    public String getPackageSrc() {
+      return packageSrc;
+    }
+    public String summary() {
+      return url+(version == null ? "" : "|"+version)+(packageSrc != null ? "("+packageSrc+")" : "");
+    }
+    
+    
+  }
+
+  public class OIDSummary {
+    private Set<OIDDefinition> definitions;
+    private Set<String> urls = new HashSet<>();
+
+    protected OIDSummary(Set<OIDDefinition> definitions) {
+      super();
+      this.definitions = definitions;
+      for (OIDDefinition d : definitions) {
+        urls.add(d.getUrl());
+      }
+    }
+
+    public Set<OIDDefinition> getDefinitions() {
+      return definitions;
+    }
+
+    public String describe() {
+      CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
+      for (OIDDefinition d : definitions) {
+        b.append(d.summary());
+      }
+      return b.toString();
+    }
+
+    public String chooseBestUrl() {
+      for (OIDDefinition d : definitions) {
+        if (d.getPackageSrc() == null) {
+          return d.getUrl();
+        }
+      }
+      for (OIDDefinition d : definitions) {
+        if (d.getUrl().startsWith("http://hl7.org/fhir/")) {
+          return d.getUrl();
+        }
+      }
+      for (OIDDefinition d : definitions) {
+        if (!d.getUrl().contains("vsac")) {
+          return d.getUrl();
+        }
+      }
+      return null;
+    }
+
+    public int urlCount() {
+      return urls.size();
+    }
+
+    public String getUrl() {
+      return urls.iterator().next();
+    }
+  }
   /**
    * Get the version of the base definitions loaded in context
    * This *does not* have to be 5.0 (R5) - the context can load other versions
@@ -634,7 +724,13 @@ public interface IWorkerContext {
   public boolean isForPublication();
   public void setForPublication(boolean value);
 
-  public Set<String> urlsForOid(boolean codeSystem, String oid);
+  /**
+   * 
+   * @param oid
+   * @param resourceType - null to search on all resource types
+   * @return
+   */
+  public OIDSummary urlsForOid(String oid, String resourceType);
 
   /**
    * this first does a fetch resource, and if nothing is found, looks in the 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/OidIndexBuilder.java

@@ -6,6 +6,7 @@ import java.sql.DriverManager;
 import java.sql.PreparedStatement;
 import java.sql.SQLException;
 import java.sql.Statement;
+import java.sql.Types;
 import java.util.HashSet;
 import java.util.Set;
 
@@ -33,11 +34,13 @@ public class OidIndexBuilder {
       Statement stmt = db.createStatement();
       stmt.execute("CREATE TABLE OIDMap (\r\n"+
           "OID            nvarchar NOT NULL,\r\n"+
+          "TYPE           nvarchar NOT NULL,\r\n"+
           "URL            nvarchar NOT NULL,\r\n"+
+          "VERSION        nvarchar NOT NULL,\r\n"+
           "Status         nvarchar NOT NULL,\r\n"+
           "PRIMARY KEY (OID, URL))\r\n");
 
-      PreparedStatement psql = db.prepareStatement("Insert into OIDMap (OID, URL, Status) values (?, ?, ?)");;
+      PreparedStatement psql = db.prepareStatement("Insert into OIDMap (OID, TYPE, URL, VERSION, Status) values (?, ?, ?, ?, ?)");
       for (File f : folder.listFiles()) {
         if (!f.getName().startsWith(".") && f.getName().endsWith(".json")) {
           try {
@@ -61,6 +64,7 @@ public class OidIndexBuilder {
       Set<String> oids = new HashSet<String>();
       String url = null;
       String status = json.asString("status");
+      String version = json.asString("version");
       if ("NamingSystem".equals(rt)) {        
         for (JsonObject id : json.getJsonObjects("uniqueId")) {
           String t = id.asString("type");
@@ -73,7 +77,7 @@ public class OidIndexBuilder {
         }
         if (url != null) {
           for (String s : oids) {
-            addOid(psql, matches, s, url, status);
+            addOid(psql, matches, s, rt, url, version, status);
           }
         }
       } else {            
@@ -97,7 +101,7 @@ public class OidIndexBuilder {
           }
           if (!oids.isEmpty()) {
             for (String s : oids) {
-              addOid(psql, matches, s, url, status);
+              addOid(psql, matches, s, rt, url, version, status);
             }
           }
         }
@@ -105,13 +109,19 @@ public class OidIndexBuilder {
     }
   }
 
-  private void addOid(PreparedStatement psql, Set<String> matches, String oid, String url, String status) throws SQLException {
+  private void addOid(PreparedStatement psql, Set<String> matches, String oid, String type, String url, String version, String status) throws SQLException {
     String key = oid+"@"+url;
     if (!matches.contains(key)) {
       matches.add(key);
       psql.setString(1, oid);
-      psql.setString(2, url);
-      psql.setString(3, status);
+      psql.setString(2, type);
+      psql.setString(3, url);
+      if (version == null) {
+        psql.setNull(4, Types.NVARCHAR);
+      } else {
+        psql.setString(4, version);  
+      }
+      psql.setString(5, status);
       psql.execute();
     }
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java

@@ -509,7 +509,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
     
     String of = pi.getFolders().get("package").getFolderPath();
     if (of != null) {
-      oidSources.add(new OIDSource(of));
+      oidSources.add(new OIDSource(of, pi.vid()));
     }
     
     if ((types == null || types.size() == 0) &&  loader != null) {