Merge branch 'release/v19.7.3'

bin/docker-build.sh

@@ -34,12 +34,6 @@ if [ "$1" = "-h" ] || [ "$1" = "--help" ]; then
 fi
 
 
-# Create env_file if it doesn't exist
-cp \
-    --no-clobber \
-    "${repo_path}/docker/portal.env.default" \
-    "${repo_path}/docker/portal.env"
-
 # Use .gitignore as .dockerignore during build only
 # not worth the effort to maintain both, for now
 copy_output="$(
@@ -49,12 +43,21 @@ copy_output="$(
         "${repo_path}/.gitignore" \
         "${repo_path}/.dockerignore"
 )"
+
+# "->" will appear in `cp` output if file is sucessfully copied
 file_copied="$(echo "$copy_output" | grep "\->" || true)"
 
 # docker-compose commands must be run in the same directory as docker-compose.yaml
 docker_compose_directory="${repo_path}/docker"
 cd "${docker_compose_directory}"
 
+
+default_portal_env="${PORTAL_ENV_FILE:-portal.env}"
+
+# Create required env_file if it doesn't exist
+cp --no-clobber portal.env.default "$default_portal_env"
+
+
 # use trap to cleanup generated .dockerignore on early exit
 trap 'cleanup_generated_dockerignore "$file_copied"; exit' INT TERM EXIT
 echo "Building portal docker image..."

docker/docker-compose.yaml

@@ -49,7 +49,7 @@ services:
     <<: *service_base
     command: bash -c '
       (wait-for-it --host=redis --port=6379 --strict -- flask set-celery-beat-healthy) &
-      wait-for-it --timeout=120 --host=web --port="$$PORT" --strict --
+      wait-for-it --timeout=120 --host=web --port=$$PORT --strict --
         celery beat
           --app portal.celery_worker.celery
           --loglevel debug

docs/source/docker.rst

@@ -120,7 +120,11 @@ If you would like to use docker to work on the portal, you can configure ``docke
 
     docker-compose up web
 
-This will mount your checkout into a docker container and use the flask development server instead of the production default (gunicorn).
+This will mount your checkout into a docker container and use the flask development server instead of the default (gunicorn).
+
+.. note::
+    Migrations and static DB values will not be automatically updated. Run ``flask sync`` as needed
+
 
 Environment Variables
 ---------------------

portal/config/eproms/Organization.json

@@ -1987,6 +1987,34 @@
       },
       "resourceType": "Organization"
     },
+    {
+      "extension": [
+        {
+          "timezone": "Europe/London",
+          "url": "http://hl7.org/fhir/StructureDefinition/user-timezone"
+        },
+        {
+          "research_protocols": [
+			{"name": "IRONMAN v3"}
+          ],
+          "url": "http://us.truenth.org/identity-codes/research-protocol"
+        }
+      ],
+      "id": 14620,
+      "identifier": [
+        {
+          "system": "http://pcctc.org/",
+          "use": "secondary",
+          "value": "146-20"
+        }
+      ],
+      "language": "en_GB",
+      "name": "University Hospital Southampton NHS Foundation Trust",
+      "partOf": {
+        "reference": "api/organization/26000"
+      },
+      "resourceType": "Organization"
+    },
     {
       "id": 30000,
       "identifier": [

portal/config/gil/Organization.json

@@ -1586,6 +1586,136 @@
         "reference": "api/organization/40001"
       },
       "resourceType": "Organization"
+    },
+    {
+      "extension": [
+        {
+          "timezone": "America/New_York",
+          "url": "http://hl7.org/fhir/StructureDefinition/user-timezone"
+        }
+      ],
+      "id": 40011,
+      "identifier": [
+        {
+          "system": "http://us.truenth.org/identity-codes/practice-region",
+          "use": "secondary",
+          "value": "state:MI"
+        },
+        {
+          "system": "http://us.truenth.org/identity-codes/shortname",
+          "use": "secondary",
+          "value": "Urologic Clinic of Southeast Michigan"
+        }
+      ],
+      "name": "Urologic Clinic of Southeast Michigan",
+      "partOf": {
+        "reference": "api/organization/40001"
+      },
+      "resourceType": "Organization"
+    },
+    {
+      "extension": [
+        {
+          "timezone": "America/New_York",
+          "url": "http://hl7.org/fhir/StructureDefinition/user-timezone"
+        }
+      ],
+      "id": 40012,
+      "identifier": [
+        {
+          "system": "http://us.truenth.org/identity-codes/practice-region",
+          "use": "secondary",
+          "value": "state:MI"
+        },
+        {
+          "system": "http://us.truenth.org/identity-codes/shortname",
+          "use": "secondary",
+          "value": "Lansing Institute of Urology"
+        }
+      ],
+      "name": "Lansing Institute of Urology",
+      "partOf": {
+        "reference": "api/organization/40001"
+      },
+      "resourceType": "Organization"
+    },
+    {
+      "extension": [
+        {
+          "timezone": "America/New_York",
+          "url": "http://hl7.org/fhir/StructureDefinition/user-timezone"
+        }
+      ],
+      "id": 40013,
+      "identifier": [
+        {
+          "system": "http://us.truenth.org/identity-codes/practice-region",
+          "use": "secondary",
+          "value": "state:MI"
+        },
+        {
+          "system": "http://us.truenth.org/identity-codes/shortname",
+          "use": "secondary",
+          "value": "Lakeshore Urology"
+        }
+      ],
+      "name": "Lakeshore Urology",
+      "partOf": {
+        "reference": "api/organization/40001"
+      },
+      "resourceType": "Organization"
+    },
+    {
+      "extension": [
+        {
+          "timezone": "America/New_York",
+          "url": "http://hl7.org/fhir/StructureDefinition/user-timezone"
+        }
+      ],
+      "id": 40014,
+      "identifier": [
+        {
+          "system": "http://us.truenth.org/identity-codes/practice-region",
+          "use": "secondary",
+          "value": "state:MI"
+        },
+        {
+          "system": "http://us.truenth.org/identity-codes/shortname",
+          "use": "secondary",
+          "value": "Wayne State University Physicians Group - Urology"
+        }
+      ],
+      "name": "Wayne State University Physicians Group - Urology",
+      "partOf": {
+        "reference": "api/organization/40001"
+      },
+      "resourceType": "Organization"
+    },
+    {
+      "extension": [
+        {
+          "timezone": "America/New_York",
+          "url": "http://hl7.org/fhir/StructureDefinition/user-timezone"
+        }
+      ],
+      "id": 40015,
+      "identifier": [
+        {
+          "system": "http://us.truenth.org/identity-codes/practice-region",
+          "use": "secondary",
+          "value": "state:MI"
+        },
+        {
+          "system": "http://us.truenth.org/identity-codes/shortname",
+          "use": "secondary",
+          "value": "Bay Area Urology"
+        }
+      ],
+      "name": "Bay Area Urology",
+      "partOf": {
+        "reference": "api/organization/40001"
+      },
+      "resourceType": "Organization"
     }
   ],
   "id": "SitePersistence v0.2",

portal/migrations/versions/29ddc9e0f61d_.py

@@ -0,0 +1,26 @@
+"""add 'failsafe' to encounter auth_methods
+
+Revision ID: 29ddc9e0f61d
+Revises: a97e02e09733
+Create Date: 2019-06-11 12:16:10.433037
+
+"""
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = '29ddc9e0f61d'
+down_revision = 'a97e02e09733'
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.execute("commit")  # get around transaction warnings by faking a commit
+    op.execute(
+        "ALTER TYPE auth_methods ADD VALUE IF NOT EXISTS 'failsafe'")
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    pass
+    # ### end Alembic commands ###

portal/models/auth.py

@@ -7,6 +7,7 @@
 from sqlalchemy import UniqueConstraint
 from sqlalchemy.dialects.postgresql import ENUM
 
+from ..audit import auditable_event
 from ..database import db
 from ..date_tools import FHIR_datetime
 from ..extensions import oauth
@@ -47,6 +48,20 @@ def as_fhir(self):
                 system=TRUENTH_IDENTITY_SYSTEM, provider=self.provider),
             'value': self.provider_id}
 
+    def reassign_owner(self, target_owner_id):
+        """For invited user flows, the auth needs to follow original user
+
+        Used specifically when an auth_provider row needs to migrate from
+        a temporary account (generated during the registration process) is
+        merged back into the initial account.
+
+        """
+        auditable_event("reassign {} auth from user {} to user {}".format(
+            self.provider, self.id, target_owner_id),
+            user_id=self.user_id, subject_id=target_owner_id,
+            context='authentication')
+        self.user_id = target_owner_id
+
 
 class AuthProviderPersistable(AuthProvider):
     """For persistence to function, need instance serialization

portal/models/encounter.py

@@ -34,7 +34,7 @@ class EncounterCodings(db.Model):
 auth_method_types = ENUM(
     'password_authenticated', 'url_authenticated', 'staff_authenticated',
     'staff_handed_to_patient', 'service_token_authenticated',
-    'url_authenticated_and_verified',
+    'url_authenticated_and_verified', 'failsafe',
     name='auth_methods', create_type=False)
 
 
@@ -178,6 +178,7 @@ def initiate_encounter(user, auth_method):
         start_time=datetime.utcnow(), user_id=user.id)
     db.session.add(encounter)
     db.session.commit()
+    return db.session.merge(encounter)
 
 
 def finish_encounter(user):

portal/models/user.py

@@ -37,7 +37,7 @@
 from .audit import Audit
 from .codeable_concept import CodeableConcept
 from .coding import Coding
-from .encounter import Encounter
+from .encounter import Encounter, initiate_encounter
 from .extension import CCExtension, TimezoneExtension
 from .fhir import bundle_results, v_or_first, v_or_n
 from .identifier import Identifier, UserIdentifier
@@ -403,15 +403,18 @@ def display_name(self):
 
     @property
     def current_encounter(self):
-        """Shortcut to current encounter, if present
+        """Shortcut to current encounter, generate failsafe if not found
 
         An encounter is typically bound to the logged in user, not
         the subject, if a different user is performing the action.
         """
         query = Encounter.query.filter(Encounter.user_id == self.id).filter(
             Encounter.status == 'in-progress')
         if query.count() == 0:
-            return None
+            current_app.logger.error(
+                "Failed to locate in-progress encounter for {}"
+                "; generate failsafe".format(self))
+            return initiate_encounter(self, auth_method='failsafe')
         if query.count() != 1:
             # Not good - we should only have one `active` encounter for
             # the current user.  Log details for debugging and return the
@@ -1508,6 +1511,11 @@ def merge_with(self, other_id):
             for item in append_list:
                 self_entity.append(item)
 
+        # If other user has an external (3rd party) auth_provider, reassign
+        # to self
+        for ap in other.auth_providers:
+            ap.reassign_owner(self.id)
+
     def promote_to_registered(self, registered_user):
         """Promote a weakly authenticated account to a registered one"""
         assert self.id != registered_user.id

portal/static/js/forceReload.js

@@ -0,0 +1,4 @@
+window.onload = function() {
+    window.location.reload(true);
+};
+window.onload();