bring dev changes into main for release 24.07.01 (#68)

* Migration update (#65) * WIP: starting migration work * WIP: run_migration CLI * Moving the migration into separate module * WIP: migration class * WIP: separating migratory functionality * WIP: fixing naming * Refactoring and adding mock tests * Modifying tests * WIP: fixing tests * WIP: fixing tests * WIP: tests * WIP: fixing tests * WIP: fixing test * Fixing tests * WIP: fixing tests * WIP: fixing errors * Fixing formatting * Addressing comments * Tests * WIP: fixing tests * WIP: fixing test * Fixing tests * WIP: working single tree * Changed the migration from referencing the latest applied to the latest created file (Reversable) * Only allow migreation to be generated, if the system is caught up * WIP: adding testing * Removing tests * Adding back the test case * Fixing upgrade * Fixing a test * Changed to linked list * WIP: adding test * WIP: testing * WIP: testing * WIP: testing * Fixing cycles * WIP: adding eq * Fixing cycles * WIP: fixing cycles * WIP: fixing migration * WIP: fixing * WIP: fixing migration * WIP: fixing migration * Testing cycle * errors * Fixing errors * errors * errors * Refactoring Linked List utilities * WIP: fixing cycles * WIP: fixing cycles * Fixing cycles * Fixing data * WIP:fix * Testing * WIP: fixing errors * WIP: new * WIP: fixing errors * WIP: fixing cycle * WIP: fixing errors * Fixing errors * WIP: fixing erros * WIp: fixing * fixing * fixing circular * Adding tests * Changing logic * utils * fix list fixture * fix * Fixing test * Responding to comments * Fixing add * Adding comments * Fixing tests * Fixing tests * Tests * Tests * Fixed Test * migration * Fixing tests * WIP: test * WIP: file * Fixing test * WIP: fixing * WIP: imp * WIP: imp * Removing .imp test * WIP: removing test * Adding property * Decoupling name from version * Enforce unique migration names * Fixing test * Adding errors * Testing added * Fixing tests * Errors * New version * Adding tests * Fixing * Adding tests * Tests * Modifying tests * test * Fixing tests * Added example * Small adjusments to the text * Addressing comments WIP: put * Constant system comparison * Adding temporary function to test direct PUT that is failing from within the code. * Left an exception where the implementation doesn't match the spec * Ported away from HAPI_request, preferring requests on this module. Eliminated a number of repeated strings using common variables Use logging rather than print When including query string parameters, use built in function parameters, as special characters need to be URL encoded. * Fixing * Removing test * Made migrations more robust * Removing isacc * Changing default number to uuid --------- Co-authored-by: Paul F Bugni <[email protected]> * Migration moving (#67) Changing the isacc to reference the package instead. Requirements.txt will work when we update the fhir-migration package at main --------- Co-authored-by: Daniil <[email protected]>
uwcirg · Jul 1, 2024 · bdc6a8e · bdc6a8e
1 parent 9edc802
commit bdc6a8e
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Showing 5 changed files with 34 additions and 6 deletions.
diff --git a/isacc_messaging/api/isacc_record_creator.py b/isacc_messaging/api/isacc_record_creator.py
@@ -67,7 +67,6 @@ def dispatch_cr(self, cr: CommunicationRequest):
             if not patient.generalPractitioner:
                 practitioner=None
             else:
-
                 practitioner = resolve_reference(patient.generalPractitioner[0].reference)
             expanded_payload = expand_template_args(
                 content=cr.payload[0].contentString,
@@ -418,6 +417,6 @@ def execute_requests(self) -> Tuple[List[dict], List[dict]]:
 
         return successes, errors
 
-    def process_cr(self, cr: CommunicationRequest, successes: list):
+    def process_cr(self, cr: CommunicationRequest):
         status, statusReason = self.dispatch_cr(cr=cr)
-        return status, statusReason
+        return status, statusReason
diff --git a/isacc_messaging/api/views.py b/isacc_messaging/api/views.py
@@ -11,7 +11,6 @@
 
 base_blueprint = Blueprint('base', __name__, cli_group=None)
 
-
 @base_blueprint.route('/')
 def root():
     return {'ok': True}
@@ -302,3 +301,4 @@ def deactivate_patient(patient_id):
         f"Patient {patient_id} active set to false",
         level='info'
     )
+
diff --git a/isacc_messaging/app.py b/isacc_messaging/app.py
@@ -4,11 +4,11 @@
 import os
 from werkzeug.middleware.proxy_fix import ProxyFix
 
+from fhir_migrations import commands as migration_commands
 from isacc_messaging.api import views
 from isacc_messaging.audit import audit_entry, audit_log_init
 from isacc_messaging.extensions import oauth
 
-
 def create_app(testing=False, cli=False):
     """Application factory, used to create application
     """
@@ -58,6 +58,7 @@ def register_blueprints(app):
     """register all blueprints for application
     """
     app.register_blueprint(views.base_blueprint)
+    app.register_blueprint(migration_commands.migration_blueprint)
 
 
 def configure_proxy(app):

diff --git a/requirements.txt b/requirements.txt
@@ -39,4 +39,5 @@ torch==1.13.0
 transformers==4.24.0
 scipy==1.7.3
 numpy==1.21.5
-pandas==1.3.5
+pandas==1.3.5
+git+https://github.com/uwcirg/fhir-migrations
diff --git a/tests/test_app.py b/tests/test_app.py
@@ -0,0 +1,27 @@
+import unittest
+from isacc_messaging.app import create_app
+
+class TestConfig:
+    TESTING = True
+    LOG_LEVEL = 'DEBUG'
+    LOGSERVER_URL = None
+    LOGSERVER_TOKEN = None
+    VERSION_STRING = 'test_version'
+    PREFERRED_URL_SCHEME = 'http'
+
+
+class TestIsaccMessagingApp(unittest.TestCase):
+    def setUp(self):
+        self.app = create_app(testing=True)
+        self.app.config.from_object(TestConfig)
+        self.client = self.app.test_client()
+
+    def test_app_exists(self):
+        self.assertIsNotNone(self.app)
+
+    def test_blueprints_registered(self):
+        self.assertIn('base', self.app.blueprints)
+        self.assertIn('migration', self.app.blueprints)
+
+if __name__ == '__main__':
+    unittest.main()