From c51678bae6ab129010be3df0dd3d5607735ad75b Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Fri, 20 Jul 2018 00:26:32 -0400
Subject: [PATCH 01/28] v5.10.0-beta.1

---
 package.json | 4 ++--
 yarn.lock    | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/package.json b/package.json
index d5dff8d..4fdaaba 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "shr-cli",
-  "version": "5.9.1",
+  "version": "5.10.0-beta.1",
   "description": "Command-line interface for SHR tools",
   "author": "",
   "license": "Apache-2.0",
@@ -23,7 +23,7 @@
     "mkdirp": "^0.5.1",
     "shr-es6-export": "^5.4.1",
     "shr-expand": "^5.5.1",
-    "shr-fhir-export": "^5.6.1",
+    "shr-fhir-export": "^5.7.0-beta.1",
     "shr-json-export": "^5.1.4",
     "shr-json-javadoc": "^1.4.2",
     "shr-json-schema-export": "^5.3.0",
diff --git a/yarn.lock b/yarn.lock
index d2c4885..1430e37 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -927,9 +927,9 @@ shr-expand@^5.5.1:
   version "5.5.1"
   resolved "https://registry.yarnpkg.com/shr-expand/-/shr-expand-5.5.1.tgz#e8d3c0cebe9bf05d663f2e90d7ff439b39f1a82c"
 
-shr-fhir-export@^5.6.1:
-  version "5.6.1"
-  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.6.1.tgz#acb6380380d7b626c7d8b73cd8358d035fcc6e98"
+shr-fhir-export@^5.7.0-beta.1:
+  version "5.7.0-beta.1"
+  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0-beta.1.tgz#a02836faad26597e56de15b487ace1c61e9f0fa6"
   dependencies:
     fs-extra "^2.0.0"
     lodash "^4.17.5"

From 42877a8fa395fa3deb75502ead85900daf78d071 Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Mon, 23 Jul 2018 09:15:22 -0400
Subject: [PATCH 02/28] Fix CIMCORE when numbers of mapping targets != 1

If there were no mappings, then the CIMCORE exporter would crash.

If there were mappings for more than 1 target, then only the 1st target would be processed.

Both of these issues are now fixed.
---
 app.js | 30 ++++++++++++++++++------------
 1 file changed, 18 insertions(+), 12 deletions(-)

diff --git a/app.js b/app.js
index e97db27..63ee84f 100644
--- a/app.js
+++ b/app.js
@@ -193,18 +193,24 @@ if (doCIMCORE) {
     }
 
     //mappings
-    for (const mapping of [...expSpecifications.maps._targetMap][0][1].all) {
-      let namespace = mapping.identifier.namespace.replace(/\./, '-');
-      let name = mapping.identifier.name;
-      let out = Object.assign({ 'fileType': 'Mapping' }, mapping.toJSON());
-      cimcoreSpecifications.mappings.push(out);
-
-      const hierarchyPath = `${baseCIMCOREPath}/${namespace}/mappings/${name}-mapping.json`;
-      try {
-        mkdirp.sync(hierarchyPath.substring(0, hierarchyPath.lastIndexOf('/')));
-        fs.writeFileSync(hierarchyPath, JSON.stringify(out, null, '  '));
-      } catch (error) {
-        logger.error('Unable to successfully serialize mapping %s into CIMCORE, failing with error "%s". ERROR_CODE:15003', mapping.identifier.fqn, error);
+    for (const target of expSpecifications.maps.targets) {
+      for (const mapping of expSpecifications.maps.getTargetMapSpecifications(target).all) {
+        let namespace = mapping.identifier.namespace.replace(/\./, '-');
+        let name = mapping.identifier.name;
+        if (expSpecifications.maps.targets.length > 1) {
+          // Need to add the target to the name to make it unique
+          name += `-${target}`;
+        }
+        let out = Object.assign({ 'fileType': 'Mapping' }, mapping.toJSON());
+        cimcoreSpecifications.mappings.push(out);
+
+        const hierarchyPath = path.join(baseCIMCOREPath, namespace, 'mappings', `${name}-mapping.json`);
+        try {
+          mkdirp.sync(hierarchyPath.substring(0, hierarchyPath.lastIndexOf('/')));
+          fs.writeFileSync(hierarchyPath, JSON.stringify(out, null, '  '));
+        } catch (error) {
+          logger.error('Unable to successfully serialize mapping %s into CIMCORE, failing with error "%s". ERROR_CODE:15003', mapping.identifier.fqn, error);
+        }
       }
     }
   } catch (error) {

From db56278b60d095a0d69b7bdd9e141e3133218243 Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Mon, 23 Jul 2018 10:44:52 -0400
Subject: [PATCH 03/28] Make the mapping target part of the output path

When producing CIMCORE, put the mappings in <namespace>/mappings/<target>/.
---
 app.js | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/app.js b/app.js
index 63ee84f..9eb7f3f 100644
--- a/app.js
+++ b/app.js
@@ -197,14 +197,10 @@ if (doCIMCORE) {
       for (const mapping of expSpecifications.maps.getTargetMapSpecifications(target).all) {
         let namespace = mapping.identifier.namespace.replace(/\./, '-');
         let name = mapping.identifier.name;
-        if (expSpecifications.maps.targets.length > 1) {
-          // Need to add the target to the name to make it unique
-          name += `-${target}`;
-        }
         let out = Object.assign({ 'fileType': 'Mapping' }, mapping.toJSON());
         cimcoreSpecifications.mappings.push(out);
 
-        const hierarchyPath = path.join(baseCIMCOREPath, namespace, 'mappings', `${name}-mapping.json`);
+        const hierarchyPath = path.join(baseCIMCOREPath, namespace, 'mappings', target, `${name}-mapping.json`);
         try {
           mkdirp.sync(hierarchyPath.substring(0, hierarchyPath.lastIndexOf('/')));
           fs.writeFileSync(hierarchyPath, JSON.stringify(out, null, '  '));

From 69877d73186395a57aafad1d212e0dbda4e68959 Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Mon, 23 Jul 2018 14:41:49 -0400
Subject: [PATCH 04/28] Update shr-fhir-export to 5.7.0-beta.2

---
 package.json | 2 +-
 yarn.lock    | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/package.json b/package.json
index 4fdaaba..79b85c0 100644
--- a/package.json
+++ b/package.json
@@ -23,7 +23,7 @@
     "mkdirp": "^0.5.1",
     "shr-es6-export": "^5.4.1",
     "shr-expand": "^5.5.1",
-    "shr-fhir-export": "^5.7.0-beta.1",
+    "shr-fhir-export": "^5.7.0-beta.2",
     "shr-json-export": "^5.1.4",
     "shr-json-javadoc": "^1.4.2",
     "shr-json-schema-export": "^5.3.0",
diff --git a/yarn.lock b/yarn.lock
index 1430e37..c18dd49 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -927,9 +927,9 @@ shr-expand@^5.5.1:
   version "5.5.1"
   resolved "https://registry.yarnpkg.com/shr-expand/-/shr-expand-5.5.1.tgz#e8d3c0cebe9bf05d663f2e90d7ff439b39f1a82c"
 
-shr-fhir-export@^5.7.0-beta.1:
-  version "5.7.0-beta.1"
-  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0-beta.1.tgz#a02836faad26597e56de15b487ace1c61e9f0fa6"
+shr-fhir-export@^5.7.0-beta.2:
+  version "5.7.0-beta.2"
+  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0-beta.2.tgz#7b05d5b3aa61243b4c4c8c833ae92557351deb1c"
   dependencies:
     fs-extra "^2.0.0"
     lodash "^4.17.5"

From 7a33b78792995693bcba06ccb1445e46d2abfb28 Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Mon, 23 Jul 2018 14:42:52 -0400
Subject: [PATCH 05/28] v5.10.0-beta.2

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index 79b85c0..9d17b88 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "shr-cli",
-  "version": "5.10.0-beta.1",
+  "version": "5.10.0-beta.2",
   "description": "Command-line interface for SHR tools",
   "author": "",
   "license": "Apache-2.0",

From 65f13d28326d05bf3fbcbc0a2026094a9b86ba9d Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Mon, 6 Aug 2018 19:23:13 -0400
Subject: [PATCH 06/28] Upgrade shr-fhir-export and shr-expand to new betas

- Fixes problem constraining references
- Supports nested slicing
---
 package.json |  4 ++--
 yarn.lock    | 12 ++++++------
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/package.json b/package.json
index 9d17b88..b37a713 100644
--- a/package.json
+++ b/package.json
@@ -22,8 +22,8 @@
     "commander": "^2.9.0",
     "mkdirp": "^0.5.1",
     "shr-es6-export": "^5.4.1",
-    "shr-expand": "^5.5.1",
-    "shr-fhir-export": "^5.7.0-beta.2",
+    "shr-expand": "^5.5.2-beta.1",
+    "shr-fhir-export": "^5.7.0-beta.3",
     "shr-json-export": "^5.1.4",
     "shr-json-javadoc": "^1.4.2",
     "shr-json-schema-export": "^5.3.0",
diff --git a/yarn.lock b/yarn.lock
index c18dd49..6952860 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -923,13 +923,13 @@ shr-es6-export@^5.4.1:
   dependencies:
     reserved-words "^0.1.2"
 
-shr-expand@^5.5.1:
-  version "5.5.1"
-  resolved "https://registry.yarnpkg.com/shr-expand/-/shr-expand-5.5.1.tgz#e8d3c0cebe9bf05d663f2e90d7ff439b39f1a82c"
+shr-expand@^5.5.2-beta.1:
+  version "5.5.2-beta.1"
+  resolved "https://registry.yarnpkg.com/shr-expand/-/shr-expand-5.5.2-beta.1.tgz#25baa7e4363ebcef1734210253b17da1e4ec1d4f"
 
-shr-fhir-export@^5.7.0-beta.2:
-  version "5.7.0-beta.2"
-  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0-beta.2.tgz#7b05d5b3aa61243b4c4c8c833ae92557351deb1c"
+shr-fhir-export@^5.7.0-beta.3:
+  version "5.7.0-beta.3"
+  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0-beta.3.tgz#40b5c7e3a609bba172fbdc73deab4c29b523520d"
   dependencies:
     fs-extra "^2.0.0"
     lodash "^4.17.5"

From 22b83f1640b92deaf31524331493f053d3bc07b0 Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Mon, 6 Aug 2018 19:23:25 -0400
Subject: [PATCH 07/28] v5.10.0-beta.3

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index b37a713..be30c63 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "shr-cli",
-  "version": "5.10.0-beta.2",
+  "version": "5.10.0-beta.3",
   "description": "Command-line interface for SHR tools",
   "author": "",
   "license": "Apache-2.0",

From ffd9bc1abfdd8a92adcdce517311f6774a19a3d5 Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Tue, 7 Aug 2018 23:07:23 -0400
Subject: [PATCH 08/28] OS-independent paths

Fix all file paths to use node path to ensure proper path separators based on OS.
---
 app.js | 34 +++++++++++++++++-----------------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/app.js b/app.js
index 9eb7f3f..11f20d5 100644
--- a/app.js
+++ b/app.js
@@ -33,7 +33,7 @@ program
   .option('-l, --log-level <level>', 'the console log level <fatal,error,warn,info,debug,trace> (default: info)', /^(fatal|error|warn|info|debug|trace)$/i, 'info')
   .option('-m, --log-mode <mode>', 'the console log mode <short,long,json,off> (default: short)', /^(short|long|json|off)$/i, 'short')
   .option('-s, --skip <feature>', 'skip an export feature <fhir,json,cimcore,json-schema,es6,model-doc,all> (default: <none>)', collect, [])
-  .option('-o, --out <out>', 'the path to the output folder (default: ./out)', './out')
+  .option('-o, --out <out>', `the path to the output folder (default: ${path.join('.', 'out')})`, path.join('.', 'out'))
   .option('-c, --config <config>', 'the name of the config file (default: config.json)', 'config.json')
   .option('-d, --duplicate', 'show duplicate error messages (default: false)')
   .arguments('<path-to-shr-defs>')
@@ -130,7 +130,7 @@ if (doCIMCORE) {
       'namespaces': {},
     //also includes 'projectInfo'
     };
-    const baseCIMCOREPath = `${program.out}/cimcore/`;
+    const baseCIMCOREPath = path.join(program.out, 'cimcore');
 
     //meta project file
     let versionInfo = {
@@ -141,8 +141,8 @@ if (doCIMCORE) {
     let projectMetaOutput = Object.assign({ 'fileType': 'ProjectInfo' }, configSpecifications, versionInfo); //project meta information
     cimcoreSpecifications['projectInfo'] = projectMetaOutput;
 
-    const hierarchyPath = `${program.out}/cimcore/project.json`;
-    mkdirp.sync(hierarchyPath.substring(0, hierarchyPath.lastIndexOf('/')));
+    const hierarchyPath = path.join(program.out, 'cimcore', 'project.json');
+    mkdirp.sync(path.dirname(hierarchyPath));
     fs.writeFileSync(hierarchyPath, JSON.stringify(projectMetaOutput, null, '  '));
 
     //meta namespace files
@@ -151,9 +151,9 @@ if (doCIMCORE) {
       let out = Object.assign({ 'fileType': 'Namespace' }, ns.toJSON());
       cimcoreSpecifications.namespaces[ns.namespace] = out;
 
-      const hierarchyPath = `${baseCIMCOREPath}/${namespace}/${namespace}.json`;
+      const hierarchyPath = path.join(baseCIMCOREPath, namespace, `${namespace}.json`);
       try {
-        mkdirp.sync(hierarchyPath.substring(0, hierarchyPath.lastIndexOf('/')));
+        mkdirp.sync(path.dirname(hierarchyPath));
         fs.writeFileSync(hierarchyPath, JSON.stringify(out, null, '  '));
       } catch (error) {
         logger.error('Unable to successfully serialize namespace meta information %s into CIMCORE, failing with error "%s". ERROR_CODE:15004', namespace, error);
@@ -167,9 +167,9 @@ if (doCIMCORE) {
       let out = Object.assign({ 'fileType': 'DataElement' }, de.toJSON());
       cimcoreSpecifications.dataElements.push(out);
 
-      const hierarchyPath = `${baseCIMCOREPath}/${namespace}/${fqn}.json`;
+      const hierarchyPath = path.join(baseCIMCOREPath, namespace, `${fqn}.json`);
       try {
-        mkdirp.sync(hierarchyPath.substring(0, hierarchyPath.lastIndexOf('/')));
+        mkdirp.sync(path.dirname(hierarchyPath));
         fs.writeFileSync(hierarchyPath, JSON.stringify(out, null, '  '));
       } catch (error) {
         logger.error('Unable to successfully serialize element %s into CIMCORE, failing with error "%s". ERROR_CODE:15001', de.identifier.fqn, error);
@@ -183,9 +183,9 @@ if (doCIMCORE) {
       let out = Object.assign({ 'fileType': 'ValueSet' }, vs.toJSON());
       cimcoreSpecifications.valueSets.push(out);
 
-      const hierarchyPath = `${baseCIMCOREPath}/${namespace}/valuesets/${name}.json`;
+      const hierarchyPath = path.join(baseCIMCOREPath, namespace, 'valuesets', `${name}.json`);
       try {
-        mkdirp.sync(hierarchyPath.substring(0, hierarchyPath.lastIndexOf('/')));
+        mkdirp.sync(path.dirname(hierarchyPath));
         fs.writeFileSync(hierarchyPath, JSON.stringify(out, null, '  '));
       } catch (error) {
         logger.error('Unable to successfully serialize value set %s into CIMCORE, failing with error "%s". ERROR_CODE:15002', vs.identifier.fqn, error);
@@ -202,7 +202,7 @@ if (doCIMCORE) {
 
         const hierarchyPath = path.join(baseCIMCOREPath, namespace, 'mappings', target, `${name}-mapping.json`);
         try {
-          mkdirp.sync(hierarchyPath.substring(0, hierarchyPath.lastIndexOf('/')));
+          mkdirp.sync(path.dirname(hierarchyPath));
           fs.writeFileSync(hierarchyPath, JSON.stringify(out, null, '  '));
         } catch (error) {
           logger.error('Unable to successfully serialize mapping %s into CIMCORE, failing with error "%s". ERROR_CODE:15003', mapping.identifier.fqn, error);
@@ -220,8 +220,8 @@ if (doCIMCORE) {
 if (doJSON) {
   try {
     const jsonHierarchyResults = shrJE.exportToJSON(specifications, configSpecifications);
-    const hierarchyPath = `${program.out}/json/definitions.json`;
-    mkdirp.sync(hierarchyPath.substring(0, hierarchyPath.lastIndexOf('/')));
+    const hierarchyPath = path.join(program.out, 'json', 'definitions.json');
+    mkdirp.sync(path.dirname(hierarchyPath));
     fs.writeFileSync(hierarchyPath, JSON.stringify(jsonHierarchyResults, null, '  '));
   } catch (error) {
     logger.fatal('Failure in JSON export. Aborting with error message: %s', error);
@@ -303,7 +303,7 @@ if (doJSONSchema) {
     const baseSchemaNamespace = 'https://standardhealthrecord.org/schema';
     const baseSchemaNamespaceWithSlash = baseSchemaNamespace + '/';
     const jsonSchemaResults = shrJSE.exportToJSONSchema(expSpecifications, baseSchemaNamespace, typeURL);
-    const jsonSchemaPath = `${program.out}/json-schema/`;
+    const jsonSchemaPath = path.join(program.out, 'json-schema');
     mkdirp.sync(jsonSchemaPath);
     for (const schemaId in jsonSchemaResults) {
       const filename = `${schemaId.substring(baseSchemaNamespaceWithSlash.length).replace(/\//g, '.')}.schema.json`;
@@ -315,7 +315,7 @@ if (doJSONSchema) {
   //   const baseSchemaExpandedNamespace = 'https://standardhealthrecord.org/schema-expanded';
   //   const baseSchemaExpandedNamespaceWithSlash = baseSchemaExpandedNamespace + '/';
   //   const jsonSchemaExpandedResults = shrJSE.exportToJSONSchema(expSpecifications, baseSchemaExpandedNamespace, typeURL, true);
-  //   const jsonSchemaExpandedPath = `${program.out}/json-schema-expanded/`;
+  //   const jsonSchemaExpandedPath = path.join(program.out, 'json-schema-expanded');
   //   mkdirp.sync(jsonSchemaExpandedPath);
   //   for (const schemaId in jsonSchemaExpandedResults) {
   //     const filename = `${schemaId.substring(baseSchemaExpandedNamespaceWithSlash.length).replace(/\//g, '.')}.schema.json`;
@@ -333,8 +333,8 @@ if (doJSONSchema) {
 if (doModelDoc) {
   if (doCIMCORE) {
     try {
-      const hierarchyPath = `${program.out}/modeldoc`;
-      const fhirPath = `${program.out}/fhir/guide/pages/modeldoc`;
+      const hierarchyPath = path.join(program.out, 'modeldoc');
+      const fhirPath = path.join(program.out, 'fhir', 'guide', 'pages', 'modeldoc');
       const javadocResults = shrJDE.compileJavadoc(cimcoreSpecifications, hierarchyPath);
       shrJDE.exportToPath(javadocResults, hierarchyPath);
       if (doFHIR && configSpecifications.implementationGuide.includeModelDoc == true) {

From 72b4f8100a1c19078fa2c6ec8321988255784431 Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Tue, 7 Aug 2018 23:32:54 -0400
Subject: [PATCH 09/28] Upgrade shr-fhir-export to 5.7.0-beta.4

This updgrade brings in a new igpublisher.jar.
---
 package.json | 2 +-
 yarn.lock    | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/package.json b/package.json
index be30c63..583adab 100644
--- a/package.json
+++ b/package.json
@@ -23,7 +23,7 @@
     "mkdirp": "^0.5.1",
     "shr-es6-export": "^5.4.1",
     "shr-expand": "^5.5.2-beta.1",
-    "shr-fhir-export": "^5.7.0-beta.3",
+    "shr-fhir-export": "^5.7.0-beta.4",
     "shr-json-export": "^5.1.4",
     "shr-json-javadoc": "^1.4.2",
     "shr-json-schema-export": "^5.3.0",
diff --git a/yarn.lock b/yarn.lock
index 6952860..f016380 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -927,9 +927,9 @@ shr-expand@^5.5.2-beta.1:
   version "5.5.2-beta.1"
   resolved "https://registry.yarnpkg.com/shr-expand/-/shr-expand-5.5.2-beta.1.tgz#25baa7e4363ebcef1734210253b17da1e4ec1d4f"
 
-shr-fhir-export@^5.7.0-beta.3:
-  version "5.7.0-beta.3"
-  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0-beta.3.tgz#40b5c7e3a609bba172fbdc73deab4c29b523520d"
+shr-fhir-export@^5.7.0-beta.4:
+  version "5.7.0-beta.4"
+  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0-beta.4.tgz#c5a21bdfbf14248da47ee6387f712a3e9be88bbc"
   dependencies:
     fs-extra "^2.0.0"
     lodash "^4.17.5"

From 7220dac48567266b4123cb63bc96382a6ecfd3ae Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Tue, 7 Aug 2018 23:33:47 -0400
Subject: [PATCH 10/28] v5.10.0-beta.4

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index 583adab..c4db163 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "shr-cli",
-  "version": "5.10.0-beta.3",
+  "version": "5.10.0-beta.4",
   "description": "Command-line interface for SHR tools",
   "author": "",
   "license": "Apache-2.0",

From c974f42bf947cf7df6a72e7beffcdbe4ece49370 Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Mon, 13 Aug 2018 23:13:00 -0400
Subject: [PATCH 11/28] Update shr-fhir-export and shr-json-javadoc

shr-fhir-export to 5.7.0-beta.5
shr-json-javadoc to 1.4.3-beta.1
---
 package.json |  4 ++--
 yarn.lock    | 12 ++++++------
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/package.json b/package.json
index c4db163..2561e35 100644
--- a/package.json
+++ b/package.json
@@ -23,9 +23,9 @@
     "mkdirp": "^0.5.1",
     "shr-es6-export": "^5.4.1",
     "shr-expand": "^5.5.2-beta.1",
-    "shr-fhir-export": "^5.7.0-beta.4",
+    "shr-fhir-export": "^5.7.0-beta.5",
     "shr-json-export": "^5.1.4",
-    "shr-json-javadoc": "^1.4.2",
+    "shr-json-javadoc": "^1.4.3-beta.1",
     "shr-json-schema-export": "^5.3.0",
     "shr-models": "^5.5.2",
     "shr-text-import": "^5.4.1"
diff --git a/yarn.lock b/yarn.lock
index f016380..c69bf11 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -927,9 +927,9 @@ shr-expand@^5.5.2-beta.1:
   version "5.5.2-beta.1"
   resolved "https://registry.yarnpkg.com/shr-expand/-/shr-expand-5.5.2-beta.1.tgz#25baa7e4363ebcef1734210253b17da1e4ec1d4f"
 
-shr-fhir-export@^5.7.0-beta.4:
-  version "5.7.0-beta.4"
-  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0-beta.4.tgz#c5a21bdfbf14248da47ee6387f712a3e9be88bbc"
+shr-fhir-export@^5.7.0-beta.5:
+  version "5.7.0-beta.5"
+  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0-beta.5.tgz#d846793f9f888238b748cab6a95e7066ef6b3b51"
   dependencies:
     fs-extra "^2.0.0"
     lodash "^4.17.5"
@@ -938,9 +938,9 @@ shr-json-export@^5.1.4:
   version "5.1.4"
   resolved "https://registry.yarnpkg.com/shr-json-export/-/shr-json-export-5.1.4.tgz#9b1cc379002366db70ef529a39b8220253a860ee"
 
-shr-json-javadoc@^1.4.2:
-  version "1.4.2"
-  resolved "https://registry.yarnpkg.com/shr-json-javadoc/-/shr-json-javadoc-1.4.2.tgz#3c4e16e311e1ed0497aeceba5a829918af947e71"
+shr-json-javadoc@^1.4.3-beta.1:
+  version "1.4.3-beta.1"
+  resolved "https://registry.yarnpkg.com/shr-json-javadoc/-/shr-json-javadoc-1.4.3-beta.1.tgz#231b670a3bc7808b553d2c2239eff18d1ccc9237"
   dependencies:
     bluebird "^3.5.1"
     ejs "^2.5.7"

From 4e62bbee22baa450de5efc292d833404e6ecaf5b Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Mon, 13 Aug 2018 23:14:27 -0400
Subject: [PATCH 12/28] v5.10.0-beta.5

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index 2561e35..b7fea89 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "shr-cli",
-  "version": "5.10.0-beta.4",
+  "version": "5.10.0-beta.5",
   "description": "Command-line interface for SHR tools",
   "author": "",
   "license": "Apache-2.0",

From ea29578bf8af3a923120ebf9aef28e8b8b91a841 Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Thu, 16 Aug 2018 00:47:57 -0400
Subject: [PATCH 13/28] Update shr-fhir-export and shr-json-javadoc

shr-fhir-export 5.7.0-beta.6
shr-json-javadoc 1.4.3-beta.2
---
 package.json |  4 ++--
 yarn.lock    | 12 ++++++------
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/package.json b/package.json
index b7fea89..c1c239d 100644
--- a/package.json
+++ b/package.json
@@ -23,9 +23,9 @@
     "mkdirp": "^0.5.1",
     "shr-es6-export": "^5.4.1",
     "shr-expand": "^5.5.2-beta.1",
-    "shr-fhir-export": "^5.7.0-beta.5",
+    "shr-fhir-export": "^5.7.0-beta.6",
     "shr-json-export": "^5.1.4",
-    "shr-json-javadoc": "^1.4.3-beta.1",
+    "shr-json-javadoc": "^1.4.3-beta.2",
     "shr-json-schema-export": "^5.3.0",
     "shr-models": "^5.5.2",
     "shr-text-import": "^5.4.1"
diff --git a/yarn.lock b/yarn.lock
index c69bf11..27124db 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -927,9 +927,9 @@ shr-expand@^5.5.2-beta.1:
   version "5.5.2-beta.1"
   resolved "https://registry.yarnpkg.com/shr-expand/-/shr-expand-5.5.2-beta.1.tgz#25baa7e4363ebcef1734210253b17da1e4ec1d4f"
 
-shr-fhir-export@^5.7.0-beta.5:
-  version "5.7.0-beta.5"
-  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0-beta.5.tgz#d846793f9f888238b748cab6a95e7066ef6b3b51"
+shr-fhir-export@^5.7.0-beta.6:
+  version "5.7.0-beta.6"
+  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0-beta.6.tgz#03f9f34fc3556828654401819c6e73b346275b53"
   dependencies:
     fs-extra "^2.0.0"
     lodash "^4.17.5"
@@ -938,9 +938,9 @@ shr-json-export@^5.1.4:
   version "5.1.4"
   resolved "https://registry.yarnpkg.com/shr-json-export/-/shr-json-export-5.1.4.tgz#9b1cc379002366db70ef529a39b8220253a860ee"
 
-shr-json-javadoc@^1.4.3-beta.1:
-  version "1.4.3-beta.1"
-  resolved "https://registry.yarnpkg.com/shr-json-javadoc/-/shr-json-javadoc-1.4.3-beta.1.tgz#231b670a3bc7808b553d2c2239eff18d1ccc9237"
+shr-json-javadoc@^1.4.3-beta.2:
+  version "1.4.3-beta.2"
+  resolved "https://registry.yarnpkg.com/shr-json-javadoc/-/shr-json-javadoc-1.4.3-beta.2.tgz#3a07f86e13affd43009330e17ca45d8013eabcdb"
   dependencies:
     bluebird "^3.5.1"
     ejs "^2.5.7"

From 5732eb6b309e8ff97a4a622d8477cc85bbe2289b Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Thu, 16 Aug 2018 00:48:46 -0400
Subject: [PATCH 14/28] v5.10.0-beta.6

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index c1c239d..14d5d11 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "shr-cli",
-  "version": "5.10.0-beta.5",
+  "version": "5.10.0-beta.6",
   "description": "Command-line interface for SHR tools",
   "author": "",
   "license": "Apache-2.0",

From 0406fe1867fc13bd9f51137b14f38210ec8bc452 Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Thu, 16 Aug 2018 13:46:09 -0400
Subject: [PATCH 15/28] Fix filter to pickup missing type constraints

---
 filter.js | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/filter.js b/filter.js
index c34d144..dd0c3b6 100644
--- a/filter.js
+++ b/filter.js
@@ -26,8 +26,8 @@ class SpecificationsFilter {
     // recursively find dependencies for each data element in specifications
     // if element matches filter criteria
     for (const element of this._expSpecs.dataElements.all) {
-      if (((strategy === "element") && (target.includes(element.identifier.name)))
-      || ((strategy === "namespace") && (target.includes(element.identifier.namespace)))) {
+      if (((strategy === 'element') && (target.includes(element.identifier.name)))
+      || ((strategy === 'namespace') && (target.includes(element.identifier.namespace)))) {
         this.findDataElementDependenciesRecursive(element.identifier);
       }
     }
@@ -151,6 +151,10 @@ class SpecificationsFilter {
         });
       }
 
+      field.constraintsFilter.type.constraints.forEach(constraint => {
+        this._deDependencies.add(constraint.isA);
+      });
+
       field.constraintsFilter.includesType.constraints.forEach(constraint => {
         this._deDependencies.add(constraint.isA);
       });

From 21e02d6654becd798e589bb0e484d976a6086868 Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Thu, 16 Aug 2018 16:14:04 -0400
Subject: [PATCH 16/28] Upgrade shr-fhir-export

shr-fhir-export 5.7.0-beta.7
---
 package.json | 2 +-
 yarn.lock    | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/package.json b/package.json
index 14d5d11..c71552c 100644
--- a/package.json
+++ b/package.json
@@ -23,7 +23,7 @@
     "mkdirp": "^0.5.1",
     "shr-es6-export": "^5.4.1",
     "shr-expand": "^5.5.2-beta.1",
-    "shr-fhir-export": "^5.7.0-beta.6",
+    "shr-fhir-export": "^5.7.0-beta.7",
     "shr-json-export": "^5.1.4",
     "shr-json-javadoc": "^1.4.3-beta.2",
     "shr-json-schema-export": "^5.3.0",
diff --git a/yarn.lock b/yarn.lock
index 27124db..974c483 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -927,9 +927,9 @@ shr-expand@^5.5.2-beta.1:
   version "5.5.2-beta.1"
   resolved "https://registry.yarnpkg.com/shr-expand/-/shr-expand-5.5.2-beta.1.tgz#25baa7e4363ebcef1734210253b17da1e4ec1d4f"
 
-shr-fhir-export@^5.7.0-beta.6:
-  version "5.7.0-beta.6"
-  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0-beta.6.tgz#03f9f34fc3556828654401819c6e73b346275b53"
+shr-fhir-export@^5.7.0-beta.7:
+  version "5.7.0-beta.7"
+  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0-beta.7.tgz#3aeae6db0a59913841fac97c94a9d2a3de570118"
   dependencies:
     fs-extra "^2.0.0"
     lodash "^4.17.5"

From 4155df0c082863cdf0c47c3574222905a6e26305 Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Thu, 16 Aug 2018 16:14:41 -0400
Subject: [PATCH 17/28] v5.10.0-beta.7

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index c71552c..9ea58c3 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "shr-cli",
-  "version": "5.10.0-beta.6",
+  "version": "5.10.0-beta.7",
   "description": "Command-line interface for SHR tools",
   "author": "",
   "license": "Apache-2.0",

From fb4ff588bdab70dead878a1f8f9a7ec5c3aca991 Mon Sep 17 00:00:00 2001
From: Abhijay Saran <git@abhijay.com>
Date: Wed, 21 Mar 2018 19:03:03 -0400
Subject: [PATCH 18/28] Start of ADL exporter

Moved file write logic to adl exporter
---
 app.js | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/app.js b/app.js
index 11f20d5..46bdb6a 100644
--- a/app.js
+++ b/app.js
@@ -12,6 +12,7 @@ const shrJSE = require('shr-json-schema-export');
 const shrEE = require('shr-es6-export');
 const shrFE = require('shr-fhir-export');
 const shrJDE = require('shr-json-javadoc');
+const shrAE = require('../shr-adl-exporter');
 const LogCounter = require('./logcounter');
 const SpecificationsFilter = require('./filter');
 
@@ -51,10 +52,11 @@ if (typeof input === 'undefined') {
 // Process the skip flags
 const doFHIR = program.skip.every(a => a.toLowerCase() != 'fhir' && a.toLowerCase() != 'all');
 const doJSON = program.skip.every(a => a.toLowerCase() != 'json' && a.toLowerCase() != 'all');
-const doCIMCORE = program.skip.every(a => a.toLowerCase() != 'cimcore' && a.toLowerCase() != 'all');
 const doJSONSchema = program.skip.every(a => a.toLowerCase() != 'json-schema' && a.toLowerCase() != 'all');
 const doES6 = program.skip.every(a => a.toLowerCase() != 'es6' && a.toLowerCase() != 'all');
 const doModelDoc = program.skip.every(a => a.toLowerCase() != 'model-doc' && a.toLowerCase() != 'all');
+const doCIMCORE = program.skip.every(a => a.toLowerCase() != 'cimcore' && a.toLowerCase() != 'all');
+const doADL = program.skip.every(a => a.toLowerCase() != 'adl' && a.toLowerCase() != 'all');
 
 // Process the de-duplicate error flag
 
@@ -95,7 +97,10 @@ if (doJSONSchema) {
   shrJSE.setLogger(logger.child({module: 'shr-json-schema-export'}));
 }
 if (doModelDoc) {
-  shrJDE.setLogger(logger.child({module: 'shr-json-javadoc'}));
+  shrJDE.setLogger(logger.child({ module: 'shr-json-javadoc' }));
+}
+if (doADL) {
+  shrAE.setLogger(logger.child({module: 'shr-adl-export'}));
 }
 // NOTE: shr-es6-export does not currently support a Bunyan logger
 
@@ -217,6 +222,10 @@ if (doCIMCORE) {
   logger.info('Skipping CIMCORE export');
 }
 
+if (doADL) {
+  shrAE.generateADLtoPath(expSpecifications, configSpecifications, program.out);
+}
+
 if (doJSON) {
   try {
     const jsonHierarchyResults = shrJE.exportToJSON(specifications, configSpecifications);

From 275d9ff17857e262a212ec9b123a5da93d8e71c7 Mon Sep 17 00:00:00 2001
From: Abhijay Saran <git@abhijay.com>
Date: Fri, 10 Aug 2018 16:27:51 -0400
Subject: [PATCH 19/28] Added defensive catch

---
 app.js | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/app.js b/app.js
index 46bdb6a..c696672 100644
--- a/app.js
+++ b/app.js
@@ -223,7 +223,13 @@ if (doCIMCORE) {
 }
 
 if (doADL) {
-  shrAE.generateADLtoPath(expSpecifications, configSpecifications, program.out);
+  try {
+    shrAE.generateADLtoPath(expSpecifications, configSpecifications, program.out);
+  } catch (error) {
+    logger.fatal('Failure in ADL export. Aborting with error message: %s', error);
+  }
+} else {
+  logger.info('Skipping ADL export');
 }
 
 if (doJSON) {

From e3e7e390994663218bac3b63257b3ac5c08d19d3 Mon Sep 17 00:00:00 2001
From: Abhijay Saran <git@abhijay.com>
Date: Thu, 16 Aug 2018 06:21:44 -0700
Subject: [PATCH 20/28] Added adl skip flag

---
 app.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app.js b/app.js
index c696672..addf76e 100644
--- a/app.js
+++ b/app.js
@@ -33,7 +33,7 @@ program
   .usage('<path-to-shr-defs> [options]')
   .option('-l, --log-level <level>', 'the console log level <fatal,error,warn,info,debug,trace> (default: info)', /^(fatal|error|warn|info|debug|trace)$/i, 'info')
   .option('-m, --log-mode <mode>', 'the console log mode <short,long,json,off> (default: short)', /^(short|long|json|off)$/i, 'short')
-  .option('-s, --skip <feature>', 'skip an export feature <fhir,json,cimcore,json-schema,es6,model-doc,all> (default: <none>)', collect, [])
+  .option('-s, --skip <feature>', 'skip an export feature <fhir,json,cimcore,json-schema,es6,model-doc,adl,all> (default: <none>)', collect, [])
   .option('-o, --out <out>', `the path to the output folder (default: ${path.join('.', 'out')})`, path.join('.', 'out'))
   .option('-c, --config <config>', 'the name of the config file (default: config.json)', 'config.json')
   .option('-d, --duplicate', 'show duplicate error messages (default: false)')

From 819a33d3a0dece4b648db52ec61ec343f638fb26 Mon Sep 17 00:00:00 2001
From: Abhijay Saran <git@abhijay.com>
Date: Fri, 29 Jun 2018 13:56:59 -0400
Subject: [PATCH 21/28] Minor improvements in variables and output colors

---
 app.js | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/app.js b/app.js
index addf76e..b7b7b17 100644
--- a/app.js
+++ b/app.js
@@ -12,7 +12,7 @@ const shrJSE = require('shr-json-schema-export');
 const shrEE = require('shr-es6-export');
 const shrFE = require('shr-fhir-export');
 const shrJDE = require('shr-json-javadoc');
-const shrAE = require('../shr-adl-exporter');
+const shrAE = require('../shr-adl-bmm-exporter');
 const LogCounter = require('./logcounter');
 const SpecificationsFilter = require('./filter');
 
@@ -126,9 +126,10 @@ if (filter) {
 
 const failedExports = [];
 
+let cimcoreSpecifications;
 if (doCIMCORE) {
   try {
-    var cimcoreSpecifications = {
+    cimcoreSpecifications = {
       'dataElements': [],
       'valueSets': [],
       'mappings': [],
@@ -227,6 +228,7 @@ if (doADL) {
     shrAE.generateADLtoPath(expSpecifications, configSpecifications, program.out);
   } catch (error) {
     logger.fatal('Failure in ADL export. Aborting with error message: %s', error);
+    failedExports.push('shr-adl-bmm-export');
   }
 } else {
   logger.info('Skipping ADL export');
@@ -374,7 +376,7 @@ logger.info('Finished CLI Import/Export');
 const ftlCounter = logCounter.fatal;
 const errCounter = logCounter.error;
 const wrnCounter = logCounter.warn;
-let [errColor, errLabel, wrnColor, wrnLabel, resetColor, ftlLabel] = ['\x1b[32m', 'errors', '\x1b[32m', 'warnings', '\x1b[0m', 'fatal errors'];
+let [errColor, errLabel, wrnColor, wrnLabel, resetColor, ftlColor, ftlLabel] = ['\x1b[32m', 'errors', '\x1b[32m', 'warnings', '\x1b[0m', '\x1b[31m', 'fatal errors'];
 if (ftlCounter.count > 0) {
   // logger.fatal('');
   ftlLabel = `fatal errors (${failedExports.join(', ')})`;
@@ -392,7 +394,7 @@ if (wrnCounter.count > 0) {
 const hrend = process.hrtime(hrstart);
 console.log('------------------------------------------------------------');
 console.log('Elapsed time: %d.%ds', hrend[0], Math.floor(hrend[1]/1000000));
-if (ftlCounter.count > 0) console.log('%s%d %s%s', errColor, ftlCounter.count, ftlLabel, resetColor);
+if (ftlCounter.count > 0) console.log('%s%d %s%s', ftlColor, ftlCounter.count, ftlLabel, resetColor);
 console.log('%s%d %s%s', errColor, errCounter.count, errLabel, resetColor);
 console.log('%s%d %s%s', wrnColor, wrnCounter.count, wrnLabel, resetColor);
 console.log('------------------------------------------------------------');

From ce1cad3fecfc1ff9cfa81d5217481e1a5bc119fb Mon Sep 17 00:00:00 2001
From: Abhijay Saran <git@abhijay.com>
Date: Thu, 16 Aug 2018 12:55:59 -0700
Subject: [PATCH 22/28] Added ahead and behind indicators to switchall

---
 switch-all-branches | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/switch-all-branches b/switch-all-branches
index 91ae4b3..1c9e328 100755
--- a/switch-all-branches
+++ b/switch-all-branches
@@ -1,4 +1,12 @@
 #!/bin/bash
+
+# This tool helps manage the different SHR branches
+# It is recommended you alias it to a shorter command to ease use.
+# I have it aliased in my git config as:
+#   [alias]
+#       sa = !bash switchAllBranches
+# to easily use it as "git sa feature-branch"
+
 RED='\033[0;31m'
 GREEN='\033[0;32m'
 BLUE='\033[0;36m'
@@ -146,7 +154,10 @@ function git_branches()
         #check if repo is out of sync with remote
         remote=$(cd $sub; git branch -a | grep remotes | grep -s -m 1 $($curr_br) 2>/dev/null | tr -d '*'' ' )
         if [[ $remote != "" && -n $(cd $sub; git diff --shortstat $($curr_br)..remotes/origin/$($curr_br)) ]]; then
-          changed="${changed}${YLW}*${NC}";
+          ahead=$(cd $sub; git rev-list --left-right --count $($curr_br)...origin/$($curr_br) | cut -f 1);
+          behind=$(cd $sub; git rev-list --left-right --count $($curr_br)...origin/$($curr_br) | cut -f 2);
+
+          changed="${changed}${YLW}*${DIM} [$GREEN${ahead}↟ ${RED}${behind}↡${DIM}]$NC";
         fi
 
         # #adjust spacing if needed
@@ -165,4 +176,4 @@ function git_branches()
     echo
 }
 
-git_branches
+git_branches
\ No newline at end of file

From 0ef96170f2744b585bfbcd6bee33869da2f6740d Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Thu, 16 Aug 2018 20:42:18 -0400
Subject: [PATCH 23/28] Fix shr-adl-bmm-export reference and yarn link

Fix the require on shr-adl-bmm export to use the correct (updated) package name -- and not a relative path.
Add it to yarn link and unlink.
---
 app.js          | 2 +-
 yarn-link-all   | 5 +++++
 yarn-unlink-all | 5 +++++
 3 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/app.js b/app.js
index b7b7b17..88ba4c8 100644
--- a/app.js
+++ b/app.js
@@ -12,7 +12,7 @@ const shrJSE = require('shr-json-schema-export');
 const shrEE = require('shr-es6-export');
 const shrFE = require('shr-fhir-export');
 const shrJDE = require('shr-json-javadoc');
-const shrAE = require('../shr-adl-bmm-exporter');
+const shrAE = require('shr-adl-bmm-export');
 const LogCounter = require('./logcounter');
 const SpecificationsFilter = require('./filter');
 
diff --git a/yarn-link-all b/yarn-link-all
index 7065207..5673c24 100755
--- a/yarn-link-all
+++ b/yarn-link-all
@@ -53,6 +53,10 @@ yarn link shr-models
 yarn link shr-test-helpers
 yarn link
 
+cd ../shr-adl-bmm-export
+echo "=============== shr-adl-bmm-export ================="
+yarn link
+
 cd ../shr-cli
 echo "===================== shr-cli ======================"
 yarn link shr-models
@@ -63,3 +67,4 @@ yarn link shr-json-schema-export
 yarn link shr-json-javadoc
 yarn link shr-es6-export
 yarn link shr-fhir-export
+yarn link shr-adl-bmm-export
diff --git a/yarn-unlink-all b/yarn-unlink-all
index a3efed2..11e3180 100755
--- a/yarn-unlink-all
+++ b/yarn-unlink-all
@@ -1,6 +1,7 @@
 #!/usr/bin/env bash
 
 echo "===================== shr-cli ======================"
+yarn unlink shr-adl-bmm-export
 yarn unlink shr-fhir-export
 yarn unlink shr-es6-export
 yarn unlink shr-json-schema-export
@@ -10,6 +11,10 @@ yarn unlink shr-text-import
 yarn unlink shr-expand
 yarn unlink shr-models
 
+cd ../shr-adl-bmm-export
+echo "=============== shr-adl-bmm-export ================="
+yarn unlink
+
 cd ../shr-fhir-export
 echo "================= shr-fhir-export =================="
 yarn unlink shr-models

From 358a49bca472bc5c14bcbba990718cb4df729527 Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Fri, 17 Aug 2018 13:59:09 -0400
Subject: [PATCH 24/28] Update shr-* dependencies

shr-adl-bmm-export@^1.0.0
shr-expand@^5.5.2-beta.2
shr-fhir-export@^5.7.0-beta.8
shr-models@^5.5.3-beta.1
shr-text-import@^5.4.2-beta.1
---
 package.json |  9 +++++----
 yarn.lock    | 38 +++++++++++++++++++++++++-------------
 2 files changed, 30 insertions(+), 17 deletions(-)

diff --git a/package.json b/package.json
index 9ea58c3..1ff1cb0 100644
--- a/package.json
+++ b/package.json
@@ -21,14 +21,15 @@
     "bunyan": "^1.8.12",
     "commander": "^2.9.0",
     "mkdirp": "^0.5.1",
+    "shr-adl-bmm-export": "^1.0.0",
     "shr-es6-export": "^5.4.1",
-    "shr-expand": "^5.5.2-beta.1",
-    "shr-fhir-export": "^5.7.0-beta.7",
+    "shr-expand": "^5.5.2-beta.2",
+    "shr-fhir-export": "^5.7.0-beta.8",
     "shr-json-export": "^5.1.4",
     "shr-json-javadoc": "^1.4.3-beta.2",
     "shr-json-schema-export": "^5.3.0",
-    "shr-models": "^5.5.2",
-    "shr-text-import": "^5.4.1"
+    "shr-models": "^5.5.3-beta.1",
+    "shr-text-import": "^5.4.2-beta.1"
   },
   "devDependencies": {
     "eslint": "^4.6.1",
diff --git a/yarn.lock b/yarn.lock
index 974c483..d15126b 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -230,6 +230,10 @@ decamelize@^1.1.1:
   version "1.2.0"
   resolved "https://registry.yarnpkg.com/decamelize/-/decamelize-1.2.0.tgz#f6534d15148269b20352e7bee26f501f9a191290"
 
+dedent-js@^1.0.1:
+  version "1.0.1"
+  resolved "https://registry.yarnpkg.com/dedent-js/-/dedent-js-1.0.1.tgz#bee5fb7c9e727d85dffa24590d10ec1ab1255305"
+
 deep-is@~0.1.3:
   version "0.1.3"
   resolved "https://registry.yarnpkg.com/deep-is/-/deep-is-0.1.3.tgz#b369d6fb5dbc13eecf524f91b070feedc357cf34"
@@ -277,7 +281,7 @@ eslint-visitor-keys@^1.0.0:
   version "1.0.0"
   resolved "https://registry.yarnpkg.com/eslint-visitor-keys/-/eslint-visitor-keys-1.0.0.tgz#3f3180fb2e291017716acb4c9d6d5b5c34a6a81d"
 
-eslint@^4.6.1:
+eslint@^4.19.1, eslint@^4.6.1:
   version "4.19.1"
   resolved "https://registry.yarnpkg.com/eslint/-/eslint-4.19.1.tgz#32d1d653e1d90408854bfb296f076ec7e186a300"
   dependencies:
@@ -917,19 +921,27 @@ showdown@^1.8.6:
   dependencies:
     yargs "^10.0.3"
 
+shr-adl-bmm-export@^1.0.0:
+  version "1.0.0"
+  resolved "https://registry.yarnpkg.com/shr-adl-bmm-export/-/shr-adl-bmm-export-1.0.0.tgz#1d7cfea03f540e0da32f51131bbfa9fdcc84e1de"
+  dependencies:
+    bunyan "^1.8.12"
+    dedent-js "^1.0.1"
+    eslint "^4.19.1"
+
 shr-es6-export@^5.4.1:
   version "5.4.1"
   resolved "https://registry.yarnpkg.com/shr-es6-export/-/shr-es6-export-5.4.1.tgz#f68c17b0ca8286be92d180f0095bc21c9d41f6c3"
   dependencies:
     reserved-words "^0.1.2"
 
-shr-expand@^5.5.2-beta.1:
-  version "5.5.2-beta.1"
-  resolved "https://registry.yarnpkg.com/shr-expand/-/shr-expand-5.5.2-beta.1.tgz#25baa7e4363ebcef1734210253b17da1e4ec1d4f"
+shr-expand@^5.5.2-beta.2:
+  version "5.5.2-beta.2"
+  resolved "https://registry.yarnpkg.com/shr-expand/-/shr-expand-5.5.2-beta.2.tgz#6115591a73509a84d094a5b4f9c158a1454842ef"
 
-shr-fhir-export@^5.7.0-beta.7:
-  version "5.7.0-beta.7"
-  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0-beta.7.tgz#3aeae6db0a59913841fac97c94a9d2a3de570118"
+shr-fhir-export@^5.7.0-beta.8:
+  version "5.7.0-beta.8"
+  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0-beta.8.tgz#f85d3ae0c1a37ec968e550585ed27ef85c98efb4"
   dependencies:
     fs-extra "^2.0.0"
     lodash "^4.17.5"
@@ -951,13 +963,13 @@ shr-json-schema-export@^5.3.0:
   version "5.3.0"
   resolved "https://registry.yarnpkg.com/shr-json-schema-export/-/shr-json-schema-export-5.3.0.tgz#2b1f1dd918381c23b4ebbca9946c0dc85dc227ce"
 
-shr-models@^5.5.2:
-  version "5.5.2"
-  resolved "https://registry.yarnpkg.com/shr-models/-/shr-models-5.5.2.tgz#8871fa8626278a53dc729fc04512aaf2acf91b94"
+shr-models@^5.5.3-beta.1:
+  version "5.5.3-beta.1"
+  resolved "https://registry.yarnpkg.com/shr-models/-/shr-models-5.5.3-beta.1.tgz#7fd4a03a38b893d62bbe2309a669db71fa2940be"
 
-shr-text-import@^5.4.1:
-  version "5.4.1"
-  resolved "https://registry.yarnpkg.com/shr-text-import/-/shr-text-import-5.4.1.tgz#ee708eef697b285f5c7decda5dc982e07c58fd38"
+shr-text-import@^5.4.2-beta.1:
+  version "5.4.2-beta.1"
+  resolved "https://registry.yarnpkg.com/shr-text-import/-/shr-text-import-5.4.2-beta.1.tgz#ade670f26a51e37f079710a9db6e686d72288c5d"
   dependencies:
     antlr4 "~4.6.0"
 

From 4c48335a2cf983d1a73b6e44efc4081c358a47fa Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Fri, 17 Aug 2018 14:02:11 -0400
Subject: [PATCH 25/28] v5.10.0-beta.8

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index 1ff1cb0..a33efd5 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "shr-cli",
-  "version": "5.10.0-beta.7",
+  "version": "5.10.0-beta.8",
   "description": "Command-line interface for SHR tools",
   "author": "",
   "license": "Apache-2.0",

From f881ba6cd319ad52b43a05af5bd6905a79b3a268 Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Fri, 17 Aug 2018 15:18:20 -0400
Subject: [PATCH 26/28] Skip ADL export by default

Skip ADL export by default.  Turn it on via `-a` or `--adl` flags.
---
 README.md | 1 +
 app.js    | 7 +++++--
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 89a5c33..f8202d6 100644
--- a/README.md
+++ b/README.md
@@ -39,6 +39,7 @@ $ node . --help
     -l, --log-level <level>  the console log level <fatal,error,warn,info,debug,trace> (default: info)
     -m, --log-mode <mode>    the console log mode <short,long,json,off> (default: short)
     -s, --skip <feature>     skip an export feature <fhir,json,cimcore,json-schema,es6,model-doc,all> (default: <none>)
+    -a, --adl                run the adl exporter (default: false)
     -o, --out <out>          the path to the output folder (default: ./out)
     -c, --config <config>', 'the name of the config file (default: config.json)
     -d, --duplicate'         show duplicate error messages (default: false)
diff --git a/app.js b/app.js
index 88ba4c8..e16b689 100644
--- a/app.js
+++ b/app.js
@@ -33,7 +33,8 @@ program
   .usage('<path-to-shr-defs> [options]')
   .option('-l, --log-level <level>', 'the console log level <fatal,error,warn,info,debug,trace> (default: info)', /^(fatal|error|warn|info|debug|trace)$/i, 'info')
   .option('-m, --log-mode <mode>', 'the console log mode <short,long,json,off> (default: short)', /^(short|long|json|off)$/i, 'short')
-  .option('-s, --skip <feature>', 'skip an export feature <fhir,json,cimcore,json-schema,es6,model-doc,adl,all> (default: <none>)', collect, [])
+  .option('-s, --skip <feature>', 'skip an export feature <fhir,json,cimcore,json-schema,es6,model-doc,all>', collect, [])
+  .option('-a, --adl', 'run the adl exporter (default: false)')
   .option('-o, --out <out>', `the path to the output folder (default: ${path.join('.', 'out')})`, path.join('.', 'out'))
   .option('-c, --config <config>', 'the name of the config file (default: config.json)', 'config.json')
   .option('-d, --duplicate', 'show duplicate error messages (default: false)')
@@ -56,7 +57,9 @@ const doJSONSchema = program.skip.every(a => a.toLowerCase() != 'json-schema' &&
 const doES6 = program.skip.every(a => a.toLowerCase() != 'es6' && a.toLowerCase() != 'all');
 const doModelDoc = program.skip.every(a => a.toLowerCase() != 'model-doc' && a.toLowerCase() != 'all');
 const doCIMCORE = program.skip.every(a => a.toLowerCase() != 'cimcore' && a.toLowerCase() != 'all');
-const doADL = program.skip.every(a => a.toLowerCase() != 'adl' && a.toLowerCase() != 'all');
+
+// Process the ADL flag
+const doADL = program.adl;
 
 // Process the de-duplicate error flag
 

From c3df378a2726ef98f93da96bd13e6bc134238db8 Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Fri, 31 Aug 2018 10:28:19 -0400
Subject: [PATCH 27/28] Upgrade shr-* dependencies

---
 package.json | 18 +++++++++---------
 yarn.lock    | 54 ++++++++++++++++++++++++++--------------------------
 2 files changed, 36 insertions(+), 36 deletions(-)

diff --git a/package.json b/package.json
index a33efd5..784688e 100644
--- a/package.json
+++ b/package.json
@@ -21,15 +21,15 @@
     "bunyan": "^1.8.12",
     "commander": "^2.9.0",
     "mkdirp": "^0.5.1",
-    "shr-adl-bmm-export": "^1.0.0",
-    "shr-es6-export": "^5.4.1",
-    "shr-expand": "^5.5.2-beta.2",
-    "shr-fhir-export": "^5.7.0-beta.8",
-    "shr-json-export": "^5.1.4",
-    "shr-json-javadoc": "^1.4.3-beta.2",
-    "shr-json-schema-export": "^5.3.0",
-    "shr-models": "^5.5.3-beta.1",
-    "shr-text-import": "^5.4.2-beta.1"
+    "shr-adl-bmm-export": "^1.0.1",
+    "shr-es6-export": "^5.4.2",
+    "shr-expand": "^5.5.2",
+    "shr-fhir-export": "^5.7.0",
+    "shr-json-export": "^5.1.5",
+    "shr-json-javadoc": "^1.4.3",
+    "shr-json-schema-export": "^5.3.1",
+    "shr-models": "^5.5.3",
+    "shr-text-import": "^5.4.2"
   },
   "devDependencies": {
     "eslint": "^4.6.1",
diff --git a/yarn.lock b/yarn.lock
index d15126b..cfbef22 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -921,55 +921,55 @@ showdown@^1.8.6:
   dependencies:
     yargs "^10.0.3"
 
-shr-adl-bmm-export@^1.0.0:
-  version "1.0.0"
-  resolved "https://registry.yarnpkg.com/shr-adl-bmm-export/-/shr-adl-bmm-export-1.0.0.tgz#1d7cfea03f540e0da32f51131bbfa9fdcc84e1de"
+shr-adl-bmm-export@^1.0.1:
+  version "1.0.1"
+  resolved "https://registry.yarnpkg.com/shr-adl-bmm-export/-/shr-adl-bmm-export-1.0.1.tgz#e4272bd97dbcf6c387eaeb9a3b7a7c8acbc9a1a3"
   dependencies:
     bunyan "^1.8.12"
     dedent-js "^1.0.1"
     eslint "^4.19.1"
 
-shr-es6-export@^5.4.1:
-  version "5.4.1"
-  resolved "https://registry.yarnpkg.com/shr-es6-export/-/shr-es6-export-5.4.1.tgz#f68c17b0ca8286be92d180f0095bc21c9d41f6c3"
+shr-es6-export@^5.4.2:
+  version "5.4.2"
+  resolved "https://registry.yarnpkg.com/shr-es6-export/-/shr-es6-export-5.4.2.tgz#cda40715219c268c4ed1b79ec302e832e7044446"
   dependencies:
     reserved-words "^0.1.2"
 
-shr-expand@^5.5.2-beta.2:
-  version "5.5.2-beta.2"
-  resolved "https://registry.yarnpkg.com/shr-expand/-/shr-expand-5.5.2-beta.2.tgz#6115591a73509a84d094a5b4f9c158a1454842ef"
+shr-expand@^5.5.2:
+  version "5.5.2"
+  resolved "https://registry.yarnpkg.com/shr-expand/-/shr-expand-5.5.2.tgz#e325327b8e1a1995229c7abb1fbef4a5347b67ff"
 
-shr-fhir-export@^5.7.0-beta.8:
-  version "5.7.0-beta.8"
-  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0-beta.8.tgz#f85d3ae0c1a37ec968e550585ed27ef85c98efb4"
+shr-fhir-export@^5.7.0:
+  version "5.7.0"
+  resolved "https://registry.yarnpkg.com/shr-fhir-export/-/shr-fhir-export-5.7.0.tgz#9f87bb2f3f095e059c7f8e0bde8e47e225f7f91d"
   dependencies:
     fs-extra "^2.0.0"
     lodash "^4.17.5"
 
-shr-json-export@^5.1.4:
-  version "5.1.4"
-  resolved "https://registry.yarnpkg.com/shr-json-export/-/shr-json-export-5.1.4.tgz#9b1cc379002366db70ef529a39b8220253a860ee"
+shr-json-export@^5.1.5:
+  version "5.1.5"
+  resolved "https://registry.yarnpkg.com/shr-json-export/-/shr-json-export-5.1.5.tgz#62ee553e1ac18808ff2cea6400ba128a60fafe8a"
 
-shr-json-javadoc@^1.4.3-beta.2:
-  version "1.4.3-beta.2"
-  resolved "https://registry.yarnpkg.com/shr-json-javadoc/-/shr-json-javadoc-1.4.3-beta.2.tgz#3a07f86e13affd43009330e17ca45d8013eabcdb"
+shr-json-javadoc@^1.4.3:
+  version "1.4.3"
+  resolved "https://registry.yarnpkg.com/shr-json-javadoc/-/shr-json-javadoc-1.4.3.tgz#e317d828ca3e7eccb3e8a86848b61e6e815530f3"
   dependencies:
     bluebird "^3.5.1"
     ejs "^2.5.7"
     ncp "^2.0.0"
     showdown "^1.8.6"
 
-shr-json-schema-export@^5.3.0:
-  version "5.3.0"
-  resolved "https://registry.yarnpkg.com/shr-json-schema-export/-/shr-json-schema-export-5.3.0.tgz#2b1f1dd918381c23b4ebbca9946c0dc85dc227ce"
+shr-json-schema-export@^5.3.1:
+  version "5.3.1"
+  resolved "https://registry.yarnpkg.com/shr-json-schema-export/-/shr-json-schema-export-5.3.1.tgz#6eb8201a6c4911292db7aa15354d0ddaad902eee"
 
-shr-models@^5.5.3-beta.1:
-  version "5.5.3-beta.1"
-  resolved "https://registry.yarnpkg.com/shr-models/-/shr-models-5.5.3-beta.1.tgz#7fd4a03a38b893d62bbe2309a669db71fa2940be"
+shr-models@^5.5.3:
+  version "5.5.3"
+  resolved "https://registry.yarnpkg.com/shr-models/-/shr-models-5.5.3.tgz#bc972ba2355bd7dd35d1169c7f17332967165c65"
 
-shr-text-import@^5.4.2-beta.1:
-  version "5.4.2-beta.1"
-  resolved "https://registry.yarnpkg.com/shr-text-import/-/shr-text-import-5.4.2-beta.1.tgz#ade670f26a51e37f079710a9db6e686d72288c5d"
+shr-text-import@^5.4.2:
+  version "5.4.2"
+  resolved "https://registry.yarnpkg.com/shr-text-import/-/shr-text-import-5.4.2.tgz#4ee003bf50af1655a3bc6552aaa41e9612fba572"
   dependencies:
     antlr4 "~4.6.0"
 

From ba8e03c7567fdbda165c553c19ee32a0cb2b6849 Mon Sep 17 00:00:00 2001
From: Chris Moesel <cmoesel@mitre.org>
Date: Fri, 31 Aug 2018 10:28:32 -0400
Subject: [PATCH 28/28] v5.10.0

---
 package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/package.json b/package.json
index 784688e..a87232a 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "shr-cli",
-  "version": "5.10.0-beta.8",
+  "version": "5.10.0",
   "description": "Command-line interface for SHR tools",
   "author": "",
   "license": "Apache-2.0",