Merge branch 'master' into master

_genonce.sh

@@ -16,12 +16,12 @@ echo "$txoption"
 
 publisher=$input_cache_path/$publisher_jar
 if test -f "$publisher"; then
-	JAVA -jar $publisher -ig ig.ini $txoption $*
+	java -jar $publisher -ig ig.ini $txoption $*
 
 else
 	publisher=../$publisher_jar
 	if test -f "$publisher"; then
-		JAVA -jar $publisher -ig ig.ini $txoption $*
+		java -jar $publisher -ig ig.ini $txoption $*
 	else
 		echo IG Publisher NOT FOUND in input-cache or parent folder.  Please run _updatePublisher.  Aborting...
 	fi

_updatePublisher.bat

@@ -1,5 +1,8 @@
 @ECHO OFF
-SET dlurl=https://fhir.github.io/latest-ig-publisher/org.hl7.fhir.publisher.jar
+
+SETLOCAL
+
+SET dlurl=https://storage.googleapis.com/ig-build/org.hl7.fhir.publisher.jar
 SET publisher_jar=org.hl7.fhir.publisher.jar
 SET input_cache_path=%CD%\input-cache\
 SET skipPrompts=false
@@ -16,6 +19,15 @@ IF "%~1"=="/f" SET skipPrompts=true
 ECHO "%skipPrompts%"
 
 
+:processflags
+SET ARG=%1
+IF DEFINED ARG (
+	IF "%ARG%"=="-f" SET FORCE=true
+	IF "%ARG%"=="--force" SET FORCE=true
+	SHIFT
+	GOTO processflags
+)
+
 FOR %%x IN ("%CD%") DO SET upper_path=%%~dpx
 
 IF NOT EXIST "%input_cache_path%%publisher_jar%" (
@@ -39,28 +51,32 @@ IF NOT EXIST "%input_cache_path%%publisher_jar%" (
 )
 
 :create
+IF DEFINED FORCE (
+	MKDIR "%input_cache_path%" 2> NUL
+	GOTO:download
+)
 ECHO Will place publisher jar here: %input_cache_path%%publisher_jar%
 IF "%skipPrompts%"=="true" (
 	SET create="Y"
-	) ELSE (
+) ELSE (
 	SET /p create="Ok? (Y/N) "
-	)
+)
 IF /I %create%=="Y" (
 	MKDIR "%input_cache_path%" 2> NUL
 	GOTO:download
-	)
+)
 GOTO:done
 
 :upgrade
 IF "%skipPrompts%"=="true" (
 	SET overwrite="Y"
-	) ELSE (
+) ELSE (
 	SET /p overwrite="Overwrite %jarlocation%? (Y/N) "
-	)
+)
 
 IF /I %overwrite%=="Y" (
 	GOTO:download
-	)
+)
 GOTO:done
 
 :download
@@ -110,4 +126,6 @@ ECHO Updating this file...
 start copy /y "_updatePublisher.new.bat" "_updatePublisher.bat" ^&^& del "_updatePublisher.new.bat" ^&^& exit
 REM ============================
 
-PAUSE
+IF "%skipPrompts%"=="true" (
+  PAUSE
+}

_updatePublisher.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-dlurl=https://fhir.github.io/latest-ig-publisher/org.hl7.fhir.publisher.jar
+dlurl=https://storage.googleapis.com/ig-build/org.hl7.fhir.publisher.jar
 publisher_jar=org.hl7.fhir.publisher.jar
 input_cache_path=./input-cache/
 
@@ -9,6 +9,20 @@ if ! type "curl" > /dev/null; then
 	exit 1
 fi
 
+FORCE=false
+
+while :; do
+    case $1 in
+        -f|--force) FORCE=true ;;
+        --)
+            shift
+            break
+            ;;
+        *) break
+    esac
+    shift
+done
+
 publisher="$input_cache_path$publisher_jar"
 if test -f "$publisher"; then
 	echo "IG Publisher FOUND in input-cache"
@@ -31,15 +45,17 @@ else
 	fi
 fi
 
-if "$upgrade"; then
+if [[ "$FORCE" != true ]]; then
-	message="Overwrite $jarlocation? (Y/N) "
+  if "$upgrade"; then
-else
+    message="Overwrite $jarlocation? (Y/N) "
-	echo Will place publisher jar here: "$jarlocation"
+  else
-	message="Ok? (Y/N) "
+    echo Will place publisher jar here: "$jarlocation"
+    message="Ok (enter 'y' or 'Y' to continue, any other key to cancel)?"
+  fi
+  read -r -p "$message" response
 fi
 
-read -r -p "$message" response
+if [[ "$FORCE" == true ]] || [[ "$response" =~ ^([yY])$ ]]; then
-if [[ "$response" =~ ^([yY])$ ]]; then
 	echo "Downloading most recent publisher to $jarlocationname - it's ~100 MB, so this may take a bit"
 #	wget "https://fhir.github.io/latest-ig-publisher/org.hl7.fhir.publisher.jar" -O "$jarlocation" 
 	curl $dlurl -o "$jarlocation" --create-dirs

ig.ini

@@ -1,4 +1,50 @@
 [IG]
+# ini file for the Implementation Guide publisher
+# see comments below for instructions
+
 ig = input/myig.xml
 template = fhir.base.template
-usage-stats-opt-out = false
+
+
+
+
+##########################
+### ig.ini parameters: ###
+##########################
+
+#   ig: the name of the implementation guide resource file.
+examples:
+# ig = input/myig.xml
+# ig = input/implementationguide-example2.xml
+
+#   template: the IG template that will be used to create the implementation guide (normally be a package name, but can be a local folder).
+#   base fhir template:
+#template = fhir.base.template
+
+#    HL7 (non-FHIR) IG template:
+#template = hl7.base.template
+
+#   HL7 FHIR template:
+#template = hl7.fhir.template
+
+#   it's possible to specify a specific version of the template
+#template = fhir.base.template#0.1.0
+#   or the current version:
+#template = fhir.base.template#current
+#   if no version is specified, the publisher will take the #current version
+
+#   local templates can be used by prefixing a relative path with # :
+#template = #mylocaltemplate
+#template = #..\templates\mytesttemplate1
+
+#   local templates can also use absolute paths:
+#template = #C:\MyWork\ImplementationGuides\mytemplates\mytesttemplate1
+
+
+#   other parameters are defined in the ImplementationGuide resource:
+#   https://confluence.hl7.org/display/FHIR/Implementation+Guide+Parameters
+
+#   for more documentation on implementation guides and templates, see the FHIR Guidance ImplementationGuide 
+#   http://build.fhir.org/ig/FHIR/ig-guidance
+
+

input/cql/example.cql

@@ -0,0 +1,45 @@
+library example version '1.0.0'
+
+using FHIR version '4.0.1'
+
+include FHIRHelpers version '4.0.1'
+
+codesystem "Observation Category Codes": 'http://terminology.hl7.org/CodeSystem/observation-category'
+
+valueset "Encounter Inpatient": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.666.5.307'
+valueset "Emergency Department Visit": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.117.1.7.1.292'
+valueset "Telephone Evaluation": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1082'
+valueset "Telephone Management": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.101.12.1053'
+
+valueset "COVID-19 Screening Result": 'TBD'
+
+code "Laboratory Observation Category": 'laboratory' from "Observation Category Codes"
+
+parameter "Measurement Period" Interval<DateTime>
+
+context Patient
+
+define "Inpatient, Emergency, or Telephone Evaluation or Management Encounter":
+  (
+    [Encounter: "Encounter Inpatient"]
+      union [Encounter: "Emergency Department Visit"]
+      union [Encounter: "Telephone Evaluation"]
+      union [Encounter: "Telephone Management"]
+  ) Encounter
+    where Encounter.status = 'finished'
+      and Encounter.period during "Measurement Period"
+
+define "Initial Population":
+  exists ("Inpatient, Emergency, or Telephone Evaluation or Management Encounter")
+
+define "Denominator":
+  true
+
+define "COVID-19 Communicable Disease Screening":
+  [Observation: "COVID-19 Screening Result"] Result
+    where exists (Result.category C where C ~ "Laboratory Observation Category")
+      and Result.status in { 'final', 'amended', 'corrected' }
+      and Result.effective during "Measurement Period"
+
+define "Numerator":
+  exists ("COVID-19 Communicable Disease Screening")

input/cql/notincluded.cql

@@ -0,0 +1,3 @@
+library notincluded
+
+// Example library that doesn't get included, so results in a missed warning

input/examples/Binary-example.json

@@ -0,0 +1,5 @@
+{
+  "resourceType" : "Binary",  
+  "id" : "example",
+  "data" : "ig-loader-example.pdf"
+}

input/examples/Library-example.json

@@ -0,0 +1,15 @@
+{
+  "resourceType" : "Library",
+  "url" : "http://somewhere.org/fhir/uv/myig/Library/example",
+  "version" : "1.0.0",
+  "status" : "draft",
+  "type" : {
+    "coding" : [{
+      "system" : "http://terminology.hl7.org/CodeSystem/library-type",
+      "code" : "logic-library"
+    }]
+  },
+  "content" : [{
+    "id" : "ig-loader-example.cql"
+  }]
+}

input/history/h1.json

@@ -0,0 +1,40 @@
+{
+  "resourceType" : "Bundle",
+  "id" : "h1",
+  "type" : "collection",
+  "entry" : [{
+    "resource" : {
+	  "resourceType" : "AuditEvent",
+	  "id" : "h1-1",
+	  "type" : { 
+		"system": "http://terminology.hl7.org/CodeSystem/iso-21089-lifecycle",
+		"code" : "amend"
+	  }, 
+	  "action" : "U", 
+	  "period" : { "end" : "2015-11-30" }, 
+	  "purposeOfEvent" : [{ 
+		"text": "Add \"conductible\" property to ActRelationshipType and ParticipationType codes.for ContextConduction RIM Change. And create Concept domain CodeSystem and ValueSet for ContextConductionStyle"
+	  }],
+	  "agent" : [{ 
+		"type" : {   
+		  "coding": {
+			"system": "http://terminology.hl7.org/CodeSystem/v3-ParticipationType",
+			"code":"AUT" 
+		  }
+		},
+		"name" : "Rob Hausam"
+	  },{ 
+		"type" : {   
+		  "coding": {
+			"system": "http://terminology.hl7.org/CodeSystem/contractsignertypecodes",
+			"code":"REVIEWER" 
+		  }
+		},
+		"name" : "Vocab"
+	  }],
+	  "entity" : [{
+		"what" : { "reference" : "StructureDefinition/myObservation" }
+	  }]
+	}
+  }]
+}

input/ignoreWarnings.txt

@@ -1,13 +1,15 @@
-// Add warning and/or information messages here after you've confirmed that they aren't really a problem
+== Suppressed Messages ==
-// (And include comments like this justifying why)
 
-// This is inherited from the base resource
+# Add warning and/or information messages here after you've confirmed that they aren't really a problem
+# (And include comments like this justifying why)
+
+# This is inherited from the base resource
 WARNING: StructureDefinition/myObservation: StructureDefinition.snapshot.element[15].mapping[3].map: value should not start or finish with whitespace
 
-// We're expecting these to not match the slice - we're showing how you can use slicing to define the one repetition you want even when many repetitions might be present
+# We're expecting these to not match the slice - we're showing how you can use slicing to define the one repetition you want even when many repetitions might be present
-INFORMATION: Patient/example: Patient.name[0]: This element does not match any known slice for the profile http://somewhere.org/fhir/uv/myig/StructureDefinition/mypatient
+INFORMATION: Patient/example: Patient.name[0]: This element does not match any known slice defined in the profile http://somewhere.org/fhir/uv/myig/StructureDefinition/mypatient
-INFORMATION: Patient/example: Patient.name[1]: This element does not match any known slice for the profile http://somewhere.org/fhir/uv/myig/StructureDefinition/mypatient
+INFORMATION: Patient/example: Patient.name[1]: This element does not match any known slice defined in the profile http://somewhere.org/fhir/uv/myig/StructureDefinition/mypatient
 
-// If this was a real IG, there should be examples for these profiles too.  But it's not, and I'm lazy...
+# If this was a real IG, there should be examples for these profiles too.  But it's not, and I'm lazy...
 WARNING: http://somewhere.org/fhir/uv/myig/StructureDefinition/myObservation: The Implementation Guide contains no examples for this profile
 WARNING: http://somewhere.org/fhir/uv/myig/StructureDefinition/mypractitioner: The Implementation Guide contains no examples for this profile

input/myig.xml

@@ -38,6 +38,11 @@
   <license value="CC0-1.0"/>
   <!-- This is whatever FHIR version(s) the IG artifacts are targeting (not the version of this file, which should always be 'current release') -->
   <fhirVersion value="4.0.1"/>
+ <!-- <dependsOn>
+    <uri value="http://somethign"/>
+    <packageId value="de.basisprofil.r4"/>
+    <version value="0.9.2"/>
+  </dependsOn> -->
   <definition>
     <!-- You don't need to define any groupings.  The IGPublisher will define them for you.  You only need to do so if your IG is 'special' and it's
       inappropriate to use the defaults.  Feel free to provide feedback about the defaults... -->
@@ -47,6 +52,11 @@
       </reference>
       <description value="Overriding description because we can"/>
     </resource>
+<!--<resource>
+<reference>
+<reference value="MyLogicalModel/AS"/>
+</reference>
+</resource> -->
     <resource>
       <reference>
         <reference value="Patient/example"/>
@@ -55,6 +65,19 @@
       <description value="A simple example showing how examples are defined and referenced"/>
       <exampleCanonical value="http://somewhere.org/fhir/uv/myig/StructureDefinition/mypatient"/>
     </resource>
+    <resource>
+      <reference>
+        <reference value="Bundle/h1"/>
+      </reference>
+      <name value="History"/>
+    </resource>
+<!--    <resource>
+      <reference>
+        <reference value="Library/example"/>
+      </reference>
+      <name value="Simple library example"/>
+      <description value="A simple example showing how library is pre-loaded"/>
+    </resource> -->
     <page>
       <!-- The root will always be toc.html - the template will force it if you don't do it -->
       <nameUrl value="toc.html"/>
@@ -100,6 +123,14 @@
       <code value="find-other-resources"/>
       <value value="true"/>
     </parameter>
+    <parameter>
+      <code value="path-resource"/>
+      <value value="input\history"/>
+    </parameter>
+    <parameter>
+      <code value="path-binary"/>
+      <value value="input\cql"/>
+    </parameter>
 <!-- Uncomment one or more of these if you want to limit which syntaxes are supported or want to disable the display of mappings
     <parameter>
       <code value="excludexml"/>