OpenConceptLab/ocl_issues#1791 Add support for importing NPM packages

Dockerfile

@@ -27,7 +27,7 @@ RUN chown -R ocl:ocl $APP_HOME /temp /staticfiles
 
 WORKDIR $APP_HOME
 
-RUN apk update && apk upgrade && apk add --no-cache libpq bash curl
+RUN apk update && apk upgrade && apk add --no-cache libpq bash curl busybox-extras
 
 RUN pip install --upgrade pip
 

core/code_systems/converter.py

@@ -0,0 +1,52 @@
+from fhir.resources.codesystem import CodeSystem
+
+from core.settings import DEFAULT_LOCALE
+from core.sources.models import Source
+
+
+class CodeSystemConverter:
+    """It is intended as a replacement for serializers"""
+
+    @staticmethod
+    def can_convert_from_fhir(obj):
+        return isinstance(obj, CodeSystem) or (isinstance(obj, dict) and obj.get('resourceType') == 'CodeSystem')
+
+    @staticmethod
+    def can_convert_to_fhir(obj):
+        return isinstance(obj, Source) or (isinstance(obj, dict) and obj.get('type') == 'Source')
+
+    @staticmethod
+    def to_fhir(source):
+        if isinstance(source, dict):
+            res = source
+            res_type = res.pop('type')
+            source = Source(**res)
+            res.update({'type', res_type})
+
+        code_system = {
+            'id': source.mnemonic,
+            'status': 'retired' if source.retired else 'active' if source.released else 'draft',
+            'content': source.content_type if source.content_type else 'complete',
+            'url': source.canonical_url,
+            'title': source.name,
+            'language': source.default_locale,
+            'count': source.active_concepts,
+        }
+        return CodeSystem(**code_system).dict()
+
+    @staticmethod
+    def from_fhir(code_system):
+        if isinstance(code_system, dict):
+            code_system = CodeSystem(**code_system)
+
+        source = {
+            'type': 'Source',
+            'mnemonic': code_system.id,
+            'canonical_url': code_system.url,
+            'name': code_system.title,
+            'default_locale': code_system.language if code_system.language else DEFAULT_LOCALE,
+            'content_type': code_system.content,
+            'retired': code_system.status == 'retired',
+            'released': code_system.status == 'active',
+        }
+        return source

core/code_systems/tests.py

@@ -1,7 +1,10 @@
 import json
 
+import responses
+from fhir.resources.codesystem import CodeSystem
 from rest_framework.test import APIClient
 
+from core.code_systems.converter import CodeSystemConverter
 from core.code_systems.serializers import CodeSystemDetailSerializer
 from core.code_systems.views import CodeSystemLookupNotFoundError
 from core.common.tests import OCLTestCase
@@ -589,3 +592,18 @@ def test_unable_to_represent_as_fhir(self):
         self.assertDictEqual(serialized, {
             'resourceType': 'OperationOutcome',
             'issue': [{'severity': 'error', 'details': 'Failed to represent "/invalid/uri" as CodeSystem'}]})
+
+    def test_conversion_from_fhir(self):
+        code_system = CodeSystem(**{
+            'resourceType': 'CodeSystem',
+            'id': 'test',
+            'content': 'complete',
+            'status': 'draft'
+        })
+        source = CodeSystemConverter.from_fhir(code_system)
+        self.assertEqual(source['mnemonic'], 'test')
+
+    def test_conversion_to_fhir(self):
+        source = OrganizationSourceFactory.build(mnemonic='test')
+        code_system = CodeSystemConverter.to_fhir(source)
+        self.assertEqual(code_system['id'], 'test')

core/common/errbit.py

@@ -174,11 +174,11 @@ def xml_raw(self, etype, value, trace, limit=None, file=None):
 original_print_exception = traceback.print_exception
 
 
-def print_exception_with_errbit_logging(etype, value, tb, limit=None, file=None):
+def print_exception_with_errbit_logging(etype, value, tb, limit=None, file=None, chain=True):
     if not (etype == KeyError and str(value) == "'cid'"):
         message = ERRBIT_LOGGER.xml_raw(etype, value, tb)
         ERRBIT_LOGGER.send_message(message.encode('utf-8'))
-        original_print_exception(etype, value, tb, limit=None, file=None)
+        original_print_exception(etype, value, tb, limit=limit, file=file, chain=chain)
 
 
 traceback.print_exception = print_exception_with_errbit_logging

core/common/tasks.py

@@ -271,6 +271,23 @@ def bulk_import_inline(to_import, username, update_if_exists):
     return BulkImportInline(content=to_import, username=username, update_if_exists=update_if_exists).run()
 
 
+@app.task(base=QueueOnce, retry_kwargs={'max_retries': 0})
+def bulk_import_new(path, username, owner_type, owner, import_type='default'):
+    from core.importers.importer import Importer
+    return Importer(path, username, owner_type, owner, import_type).run()
+
+
+@app.task(retry_kwargs={'max_retries': 0})
+def bulk_import_subtask(path, username, owner_type, owner, resource_type, files):
+    from core.importers.importer import ImporterSubtask
+    return ImporterSubtask(path, username, owner_type, owner, resource_type, files).run()
+
+@app.task
+def chordfinisher(*args, **kwargs):
+    """Used for waiting for all results of a group of tasks. See Importer.run()"""
+    return "Done!"
+
+
 @app.task(bind=True, retry_kwargs={'max_retries': 0})
 def bulk_import_parts_inline(self, input_list, username, update_if_exists):
     from core.importers.models import BulkImportInline