update IG publisher to allow auto-loading of resources

git-svn-id: http://gforge.hl7.org/svn/fhir/trunk/build@12183 2f0db536-2c49-4257-a3fa-e771ed206c19

implementations/java/org.hl7.fhir.r4/src/org/hl7/fhir/r4/model/CodeSystem.java

@@ -34,6 +34,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import java.util.*;
 
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.r4.model.CodeSystem.PropertyComponent;
 import org.hl7.fhir.r4.model.Enumerations.*;
 import ca.uhn.fhir.model.api.annotation.ResourceDef;
 import ca.uhn.fhir.model.api.annotation.SearchParamDefinition;
@@ -4719,6 +4720,14 @@ public ResourceType getResourceType() {
    */
   public static final ca.uhn.fhir.rest.gclient.TokenClientParam STATUS = new ca.uhn.fhir.rest.gclient.TokenClientParam(SP_STATUS);
 
+  public PropertyComponent getProperty(String code) {
+    for (PropertyComponent pd : getProperty()) {
+      if (pd.getCode().equalsIgnoreCase(code))
+        return pd;
+    }
+    return null;
+  }
+
 
 }
 

implementations/java/org.hl7.fhir.r4/src/org/hl7/fhir/r4/model/DomainResource.java

@@ -429,6 +429,13 @@ public void checkNoModifiers(String noun, String verb) throws FHIRException {
 
   }
 
+ public void addExtension(String url, Type value) {
+   Extension ex = new Extension();
+   ex.setUrl(url);
+   ex.setValue(value);
+   getExtension().add(ex);    
+ }
+
 // end addition
 
 }

implementations/java/org.hl7.fhir.r4/src/org/hl7/fhir/r4/utils/StructureMapUtilities.java

@@ -2688,7 +2688,6 @@ public StructureMap generateMapFromMappings(StructureDefinition sd) throws IOExc
     b.append("\r\n");
     b.append(suffix);
     b.append("\r\n");
-    TextFile.stringToFile(b.toString(), "c:\\temp\\test.map");
     StructureMap map = parse(b.toString());
     map.setId(tail(map.getUrl()));
     if (!map.hasStatus())

implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/utilities/Utilities.java

@@ -1069,6 +1069,21 @@ public static int countFilesInDirectory(String dirName) {
     return i;
   }
 
+  public static String makeId(String name) {
+    StringBuilder b = new StringBuilder();
+    for (char ch : name.toCharArray()) {
+      if (ch >= 'a' && ch <= 'z')
+        b.append(ch);
+      else if (ch >= 'A' && ch <= 'Z')
+        b.append(ch);
+      else if (ch >= '0' && ch <= '9')
+        b.append(ch);
+      else if (ch == '-' || ch == '.')
+        b.append(ch);
+    }
+    return b.toString();
+  }
+
 
 
 

source/consent/consent-spreadsheet.sheet.txt

@@ -586,3 +586,159 @@
   Type = @Consent.provision
   Short Name = Nested Exception Rules
   Definition = Rules which provide exceptions to the base rule or subrules
+
+=== Sheet Search =====================================
+
+ -- Row 1 -----------------------------------
+  Name = data
+  Type = reference
+  Path = Consent.provision.data.reference
+
+ -- Row 2 -----------------------------------
+  Name = patient
+  Type = reference
+  Path = Consent.patient
+
+ -- Row 3 -----------------------------------
+  Name = identifier
+  Type = token
+  Path = Consent.identifier
+
+ -- Row 4 -----------------------------------
+  Name = organization
+  Type = reference
+  Path = Consent.organization
+
+ -- Row 5 -----------------------------------
+  Name = date
+  Type = date
+  Path = Consent.dateTime
+
+ -- Row 6 -----------------------------------
+  Name = period
+  Type = date
+  Path = Consent.provision.period
+
+ -- Row 7 -----------------------------------
+  Name = status
+  Type = token
+  Path = Consent.status
+
+ -- Row 8 -----------------------------------
+  Name = category
+  Type = token
+  Path = Consent.category
+
+ -- Row 9 -----------------------------------
+  Name = consentor
+  Type = reference
+  Path = Consent.consentingParty
+
+ -- Row 10 -----------------------------------
+  Name = source
+  Type = reference
+  Path = Consent.source[x]
+
+ -- Row 11 -----------------------------------
+  Name = actor
+  Type = reference
+  Path = Consent.provision.actor.reference
+
+ -- Row 12 -----------------------------------
+  Name = action
+  Type = token
+  Path = Consent.provision.action
+
+ -- Row 13 -----------------------------------
+  Name = securitylabel
+  Type = token
+  Path = Consent.provision.securityLabel
+
+ -- Row 14 -----------------------------------
+  Name = purpose
+  Type = token
+  Path = Consent.provision.purpose
+
+=== Sheet Profiles =====================================
+
+ -- Row 1 -----------------------------------
+  Name = Consent Extension
+  IG Name = core
+  Filename = consent-extensions.xml
+  Type = spreadsheet
+
+=== Sheet Examples =====================================
+
+ -- Row 1 -----------------------------------
+  Name = Consent-In
+  Identity = consent-example-basic
+  Description = General Consent Example
+  Filename = consent-example.xml
+
+ -- Row 2 -----------------------------------
+  Name = Consent-Out
+  Identity = consent-example-Out
+  Description = Consent withholding access
+  Filename = consent-example-Out.xml
+
+ -- Row 3 -----------------------------------
+  Name = Consent-Emergency
+  Identity = consent-example-Emergency
+  Description = Consent withholding access to data for Treatment exept for Emergency Treatment
+  Filename = consent-example-Emergency.xml
+
+ -- Row 4 -----------------------------------
+  Name = Consent-Not-This
+  Identity = consent-example-notThis
+  Description = Withhold or withdraw consent for disclosure of records related to specific domain (e.g. DI, LAB, etc.)
+  Filename = consent-example-notThis.xml
+
+ -- Row 5 -----------------------------------
+  Name = Consent-Not-Time
+  Identity = consent-example-notTime
+  Description = Withhold or withdraw consent for disclosure of a specific timeframe
+  Filename = consent-example-notTime.xml
+
+ -- Row 6 -----------------------------------
+  Name = Consent-Not-Org
+  Identity = consent-example-notOrg
+  Description = Withhold or withdraw consent for disclosure to a specific provider organization
+  Filename = consent-example-notOrg.xml
+
+ -- Row 7 -----------------------------------
+  Name = Consent-Not-Them
+  Identity = consent-example-notThem
+  Description = Withhold or withdraw consent for disclosure to a specific provider agent (an individual within an organization)
+  Filename = consent-example-notThem.xml
+
+ -- Row 8 -----------------------------------
+  Name = Consent-Not-Author
+  Identity = consent-example-notAuthor
+  Description = Withhold or withdraw consent for disclosure of records that were authored by a specific organization (or service delivery location).
+  Filename = consent-example-notAuthor.xml
+
+ -- Row 9 -----------------------------------
+  Name = Consent-Grantor
+  Identity = consent-example-grantor
+  Description = Patient grants access to a specified individual for read-only access
+  Filename = consent-example-grantor.xml
+
+ -- Row 10 -----------------------------------
+  Name = Consent from Patients Know Best
+  Identity = consent-example-pkb
+  Description = Example of Patients Know Best Usage
+  Filename = consent-example-pkb.xml
+
+ -- Row 11 -----------------------------------
+  Name = Smart on FHIR example
+  Identity = consent-example-smartonfhir
+  Description = Template for recording a Smart on FHIR Authorization
+  Filename = consent-example-smartonfhir.xml
+
+ -- Row 12 -----------------------------------
+  Name = Consent with Signature
+  Identity = consent-example-signature
+  Description = Consent Example with a signature
+  Filename = consent-example-signature.xml
+
+=== Sheet Examples =====================================

tools/java/org.hl7.fhir.igtools/src/org/hl7/fhir/igtools/publisher/FetchedFile.java

@@ -147,4 +147,7 @@ public String getTitle() {
   public void setTitle(String title) {
     this.title = title;
   }
+  public boolean matches(FetchedFile other) {
+    return this.path.equals(other.path);
+  }
 }

tools/java/org.hl7.fhir.igtools/src/org/hl7/fhir/igtools/publisher/IFetchFile.java

@@ -3,6 +3,7 @@
 import java.io.IOException;
 import java.util.List;
 
+import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.context.IWorkerContext;
 import org.hl7.fhir.r4.context.IWorkerContext.ILoggingService;
 import org.hl7.fhir.r4.model.Type;
@@ -15,7 +16,7 @@ public interface IFetchFile {
   FetchedFile fetch(Type source, FetchedFile base) throws Exception;
   FetchedFile fetchResourceFile(String name) throws Exception; 
   void setPkp(IGKnowledgeProvider pkp);
-  List<FetchedFile> scan(String sourceDir, IWorkerContext context) throws IOException;
+  List<FetchedFile> scan(String sourceDir, IWorkerContext context, boolean autoScan) throws IOException, FHIRException;
 
   public ILoggingService getLogger();
   public void setLogger(ILoggingService log);

tools/java/org.hl7.fhir.igtools/src/org/hl7/fhir/igtools/publisher/IGKnowledgeProvider.java

@@ -42,6 +42,7 @@ public class IGKnowledgeProvider implements ProfileKnowledgeProvider, ParserBase
   private List<ValidationMessage> errors;
   private JsonObject defaultConfig;
   private JsonObject resourceConfig;
+  private boolean autoPath = false;
 
   public IGKnowledgeProvider(IWorkerContext context, String pathToSpec, JsonObject igs, List<ValidationMessage> errors) throws Exception {
     super();
@@ -63,7 +64,9 @@ private void loadPaths(JsonObject igs) throws Exception {
     if (resourceConfig == null)
       throw new Exception("You must provide a list of resources in the json file");
     for (Entry<String, JsonElement> pp : resourceConfig.entrySet()) {
-      if (!pp.getKey().startsWith("_")) {
+      if (pp.getKey().equals("*")) {
+        autoPath = true;
+      } else if (!pp.getKey().startsWith("_")) {
         String s = pp.getKey();
         if (!s.contains("/"))
           throw new Exception("Bad Resource Identity - should have the format [Type]/[id]:" + s);
@@ -78,8 +81,8 @@ private void loadPaths(JsonObject igs) throws Exception {
           throw new Exception("Unexpected type in resource list - must be an object");
         JsonObject o = (JsonObject) pp.getValue();
         JsonElement p = o.get("base");
-//        if (p == null)
-//          throw new Exception("You must provide a base on each path in the json file");
+        //        if (p == null)
+        //          throw new Exception("You must provide a base on each path in the json file");
         if (p != null && !(p instanceof JsonPrimitive) && !((JsonPrimitive) p).isString())
           throw new Exception("Unexpected type in paths - base must be a string");
         p = o.get("defns");
@@ -411,4 +414,8 @@ public IWorkerContext getContext() {
     return context;
   }
 
+  public boolean isAutoPath() {
+    return autoPath;
+  }
+
 }