Merge pull request #481 from onc-healthit/development

Version 2.10.0

.gitignore

@@ -13,3 +13,4 @@ tmp/*
 .vscode/*
 resources/terminology/*
 sequence_coverage.csv
+fhir-pgdata/

Gemfile.lock

@@ -1,7 +1,7 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (5.2.3)
+    activesupport (5.2.4.3)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 0.7, < 2)
       minitest (~> 5.1)
@@ -25,7 +25,7 @@ GEM
       rake (< 13.0)
     coderay (1.1.2)
     colorize (0.8.1)
-    concurrent-ruby (1.1.5)
+    concurrent-ruby (1.1.6)
     crack (0.4.3)
       safe_yaml (~> 1.0.0)
     daemons (1.3.1)
@@ -101,7 +101,7 @@ GEM
       date_time_precision (>= 0.8)
       mime-types (>= 3.0)
       nokogiri (>= 1.10.4)
-    fhir_models (4.0.2)
+    fhir_models (4.1.0)
       bcp47 (>= 0.3)
       date_time_precision (>= 0.8)
       mime-types (>= 3.0)
@@ -115,26 +115,26 @@ GEM
     http-accept (1.7.0)
     http-cookie (1.0.3)
       domain_name (~> 0.5)
-    i18n (1.7.0)
+    i18n (1.8.5)
       concurrent-ruby (~> 1.0)
     jaro_winkler (1.5.3)
     json (1.8.6)
     json_pure (1.8.6)
     jwt (2.2.1)
     kramdown (2.1.0)
     method_source (0.9.2)
-    mime-types (3.3)
+    mime-types (3.3.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2019.0904)
+    mime-types-data (3.2020.0512)
     mini_portile2 (2.4.0)
-    minitest (5.12.2)
+    minitest (5.14.1)
     msgpack (1.3.1)
     multi_json (1.13.1)
     multi_xml (0.6.0)
     multipart-post (2.1.1)
     mustermann (1.0.3)
     netrc (0.11.0)
-    nokogiri (1.10.4)
+    nokogiri (1.10.10)
       mini_portile2 (~> 2.4.0)
     oauth2 (1.4.1)
       faraday (>= 0.8, < 0.16.0)
@@ -208,7 +208,7 @@ GEM
     tilt (2.0.10)
     time_difference (0.7.0)
       activesupport (~> 5.1)
-    tzinfo (1.2.5)
+    tzinfo (1.2.7)
       thread_safe (~> 0.1)
     unf (0.1.4)
       unf_ext
@@ -254,4 +254,4 @@ DEPENDENCIES
   webmock
 
 BUNDLED WITH
-   2.0.2
+   2.1.4

config.yml

@@ -38,7 +38,7 @@ include_extras: true
 badge_text: Community
 
 # Resource validator options: must be one of "internal" or "external". external_resource_validator_url is only used if resource_validator is set to external.
-resource_validator: internal
+resource_validator: external
 external_resource_validator_url: http://validator_service:4567
 
 # module options: one or more must be set.  The first option in the list will be checked by default

create_umls.sh

@@ -68,8 +68,42 @@ fi
 echo 'Populating mrrel table'
 sqlite3 umls.db ".import MRREL.pipe mrrel"
 
+echo 'Dropping existing mrsat table'
+sqlite3 umls.db "drop table if exists mrsat;"
+
+echo 'Creating mrsat table'
+sqlite3 umls.db "create table mrsat (
+        CUI 	char(8) NOT NULL,
+        LUI       char(8),
+        SUI       char(8),
+        METAUI    varchar(20),
+        STYPE	varchar(50) NOT NULL,
+        CODE      varchar(50),
+        ATUI      varchar(10) NOT NULL,
+        SATUI     varchar(10),
+        ATN       varchar(50),
+        SAB	      varchar(20) NOT NULL,
+        ATV       varchar(1000) NOT NULL,
+        SUPPRESS	char(1),
+        CVF	int
+      );"
+
+# Remove the last pipe from each line, and quote all the fields/escape double quotes
+# Because MRSAT has stray unescaped quotes in one of the fields
+if [ ! -e MRSAT.pipe ]
+then
+ echo 'Removing last pipe from RRF'
+ sed 's/|$//' ./resources/terminology/umls_subset/MRSAT.RRF | sed $'s/"/""/g;s/[^|]*/"&"/g' > MRSAT.pipe
+fi
+
+echo 'Populating mrsat table'
+sqlite3 umls.db ".import MRSAT.pipe mrsat"
+
+echo 'Indexing mrsat(ATN,ATV)'
+sqlite3 umls.db "create index idx_at on mrsat(ATN,ATV);"
+
 echo 'Indexing mrconso(tty)'
-sqlite3 umls.db "create index  idx_tty on mrconso (tty);"
+sqlite3 umls.db "create index  idx_tty on mrconso(tty);"
 
 echo 'Indexing mrrel(rel,sab)'
 sqlite3 umls.db "create index idx_isa on mrrel(REL,SAB);"
@@ -78,4 +112,4 @@ echo 'Indexing mrconso(aui)'
 sqlite3 umls.db "CREATE INDEX idx_aui ON mrconso(AUI);"
 
 echo 'Analyzing Database'
-sqlite3 umls.db "ANALYZE;"
+sqlite3 umls.db "ANALYZE;"

docker-compose.yml

@@ -10,7 +10,7 @@ services:
   bdt_service:
     image: infernocommunity/inferno-bdt-service
   validator_service:
-    image: infernocommunity/fhir-validator-wrapper
+    image: infernocommunity/fhir-validator-service
   nginx_server:
     image: nginx
     volumes:

generator/bdt/bdt-structure.json

@@ -577,6 +577,69 @@
       ],
       "path": "4"
     },
+    {
+      "name": "Metadata",
+      "type": "group",
+      "children": [
+        {
+          "name": "CapabilityStatement",
+          "type": "group",
+          "children": [
+            {
+              "id": "CapabilityStatement-1",
+              "name": "The CapabilityStatement instantiates the bulk-data CapabilityStatement",
+              "description": "To declare conformance with this IG, a server <b>should</b> include the following URL in its own <code>CapabilityStatement.instantiates</code>: <a target=\"_blank\" href=\"https://build.fhir.org/ig/HL7/bulk-data/CapabilityStatement-bulk-data.html\">http://hl7.org/fhir/uv/bulkdata/CapabilityStatement/bulk-data</a>. The <code>CapabilityStatement</code> should contain something like:<pre>\"instantiates\": [\n    \"http://hl7.org/fhir/uv/bulkdata/CapabilityStatement/bulk-data\"\n]</pre>",
+              "type": "test",
+              "path": "5.0.0"
+            },
+            {
+              "id": "CapabilityStatement-2",
+              "name": "Includes the token endpoint in the CapabilityStatement",
+              "description": "If a server requires SMART on FHIR authorization for access, its metadata <b>must</b> support automated discovery of OAuth2 endpoints by including a “complex” extension (that is, an extension with multiple components inside) on the <code>CapabilityStatement.rest.security</code> element. Any time a client sees this extension, it must be prepared to authorize using SMART’s OAuth2-based protocol.<br/> This test is expecting to find the in CapabilityStatement an entry like:<pre>\"rest\": [\n  {\n    \"mode\": \"server\",\n    \"security\": {\n      \"extension\": [\n        {\n          \"url\": \"http://fhir-registry.smarthealthit.org/StructureDefinition/oauth-uris\",\n          \"extension\": [\n            {\n              \"url\": \"token\",\n              \"valueUri\": \"https://someserver.org/auth/token\"\n            }\n          ]\n        }\n      ]\n    }\n  }\n]</pre>Having a CapabilityStatement is optional for bulk data servers, unless they are also FHIR servers (which they typically are). However, missing a CapabilityStatement will generate a warning here. ",
+              "type": "test",
+              "path": "5.0.1"
+            },
+            {
+              "id": "CapabilityStatement-3",
+              "name": "Check if \"export\" operation is defined in the CapabilityStatement",
+              "description": "This test expects to find in the CapabilityStatement an entry like:<pre>\"rest\": [\n  {\n    \"operation\": [\n      {\n        \"name\" : \"export\"\n      }\n    ]\n  }\n]</pre>",
+              "type": "test",
+              "path": "5.0.2"
+            },
+            {
+              "id": "CapabilityStatement-4",
+              "name": "Check if \"patient-export\" operation is defined in the CapabilityStatement",
+              "description": "This test expects to find in the CapabilityStatement an entry like:<pre>\"rest\": [\n  {\n    \"operation\": [\n      {\n        \"name\" : \"patient-export\"\n      }\n    ]\n  }\n]</pre>",
+              "type": "test",
+              "path": "5.0.3"
+            },
+            {
+              "id": "CapabilityStatement-5",
+              "name": "Check if \"group-export\" operation is defined in the CapabilityStatement",
+              "description": "This test expects to find in the CapabilityStatement an entry like:<pre>\"rest\": [\n  {\n    \"operation\": [\n      {\n        \"name\" : \"group-export\"\n      }\n    ]\n  }\n]</pre>",
+              "type": "test",
+              "path": "5.0.4"
+            }
+          ],
+          "path": "5.0"
+        },
+        {
+          "name": "Well Known SMART Configuration",
+          "type": "group",
+          "children": [
+            {
+              "id": "WellKnownSmartConfiguration-1",
+              "name": "Includes token_endpoint definition",
+              "description": "This test verifies that the server provides a <code>/.well-known/smart-configuration</code> and that a <code>token_endpoint</code> property is declared within that file.",
+              "type": "test",
+              "path": "5.1.0"
+            }
+          ],
+          "path": "5.1"
+        }
+      ],
+      "path": "5"
+    },
     {
       "name": "Status Endpoint",
       "type": "group",
@@ -586,24 +649,24 @@
           "name": "Responds with 202 for active transaction IDs",
           "description": "<p>The status endpoint should return <b>202</b> status code until the export is completed.</p>See <a target=\"_blank\" href=\"https://github.com/HL7/bulk-data/blob/master/spec/export/index.md#response---in-progress-status\">https://github.com/HL7/bulk-data/blob/master/spec/export/index.md#response---in-progress-status</a>",
           "type": "test",
-          "path": "5.0"
+          "path": "6.0"
         },
         {
           "id": "Status-02",
           "name": "Replies properly in case of error",
           "description": "Runs a set of assertions to verify that:<ul><li>The returned HTTP status code is 5XX</li><li>The server returns a FHIR OperationOutcome resource in JSON format</li></ul><p>Note that even if some of the requested resources cannot successfully be exported, the overall export operation MAY still succeed. In this case, the Response.error array of the completion response MUST be populated (see below) with one or more files in ndjson format containing FHIR OperationOutcome resources to indicate what went wrong.</p>See <a target=\"_blank\" href=\"https://github.com/HL7/bulk-data/blob/master/spec/export/index.md#response---error-status-1\">https://github.com/HL7/bulk-data/blob/master/spec/export/index.md#response---error-status-1</a>",
           "type": "test",
-          "path": "5.1"
+          "path": "6.1"
         },
         {
           "id": "Status-03",
           "name": "Generates valid status response",
           "description": "Runs a set of assertions to verify that:<ul><li>The status endpoint should return <b>200</b> status code when the export is completed</li><li>The status endpoint should respond with <b>JSON</b></li><li>The <code>expires</code> header (if set) must be valid date in the future</li><li>The JSON response contains <code>transactionTime</code> which is a valid <a target=\"_blank\" href=\"http://hl7.org/fhir/datatypes.html#instant\">FHIR instant</a></li><li>The JSON response contains the kick-off URL in <code>request</code> property</li><li>The JSON response contains <code>requiresAccessToken</code> boolean property</li><li>The JSON response contains an <code>output</code> array in which:<ul><li>Every item has valid <code>type</code> property</li><li>Every item has valid <code>url</code> property</li><li>Every item may a <code>count</code> number property</li></ul></li><li>The JSON response contains an <code>error</code> array in which:<ul><li>Every item has valid <code>type</code> property</li><li>Every item has valid <code>url</code> property</li><li>Every item may a <code>count</code> number property</li></ul></li></ul>",
           "type": "test",
-          "path": "5.2"
+          "path": "6.2"
         }
       ],
-      "path": "5"
+      "path": "6"
     }
   ]
-}
+}

generator/bdt/bdt_generator.rb

@@ -11,6 +11,7 @@ class BDTGenerator < Generator::Base
         'Patient-level export' => 'Verify the system is capable of performing a Patient-Level Export that conforms to the SMART Bulk Data IG.',
         'System-level export' => 'Verify the system is capable of performing a System-Level Export that conforms to the SMART Bulk Data IG.',
         'Group-level export' => 'Verify the system is capable of performing a Group-Level Export that conforms to the SMART Bulk Data IG.',
+        'Metadata' => 'Verify the CapabilityStatement conforms to the SMART Bulk Data IG.',
         'Status Endpoint' => 'Verify the status endpoint conforms to the SMART Bulk Data IG for Export.'
       }.freeze
 

generator/generator_base.rb

@@ -27,8 +27,17 @@ def load_resources
 
             # We should consider using the native Ruby models instead of JSON
             # There were problems with round-tripping certain SearchParameters though
-            new_resource_json = JSON.parse(File.read(resource))
+
+            begin
+              new_resource_json = JSON.parse(File.read(resource))
+            rescue JSON::ParserError
+              Inferno.logger.debug("Failed to parse JSON: #{resource}")
+              next
+            end
+
             new_resource = FHIR.from_contents(File.read(resource))
+            next unless new_resource.present?
+
             resource_by_path[resource_path(new_resource)] = new_resource_json
             type = new_resource.class.name.demodulize
             type = 'CapabilityStatement' if type == 'Conformance'