Merge branch 'release/v17.5.10'

manage.py

@@ -7,7 +7,7 @@
 import click
 
 import alembic.config
-from flask_migrate import Migrate, MigrateCommand
+from flask_migrate import Migrate
 
 from portal.app import create_app
 from portal.extensions import db
@@ -30,7 +30,13 @@
 def runserver():
     # Todo: figure out how to override default host in `flask run`
     # http://click.pocoo.org/5/commands/#overriding-defaults
-    app.run(host='0.0.0.0')
+    app.run(
+        host='0.0.0.0',
+        threaded=True,
+        use_debugger=True,
+        use_reloader=True,
+    )
+
 
 def _run_alembic_command(args):
     """Helper to manage working directory and run given alembic commands"""
@@ -73,16 +79,17 @@ def sync():
         db.create_all()
     stamp_db()
     upgrade_db()
-    seed(include_interventions=True)
+    seed()
 
 
-@click.option('--include_interventions', '-i', default=False, help='Include (overwrite) intervention data')
+@click.option('--exclude_interventions', '-e', default=False,
+              help="Exclude (don't overwrite) intervention data")
 @click.option('--keep_unmentioned', '-k', default=False, help='Keep orgs and interventions not mentioned in persistence file')
 @app.cli.command(name="seed")
-def seed_command(include_interventions, keep_unmentioned):
-    seed(include_interventions, keep_unmentioned)
+def seed_command(exclude_interventions, keep_unmentioned):
+    seed(exclude_interventions, keep_unmentioned)
 
-def seed(include_interventions=False, keep_unmentioned=False):
+def seed(exclude_interventions=False, keep_unmentioned=False):
     """Seed database with required data"""
 
     # Request context necessary for generating data from own HTTP APIs
@@ -98,10 +105,10 @@ def seed(include_interventions=False, keep_unmentioned=False):
 
     # Always update interventions on development systems
     if app.config["SYSTEM_TYPE"].lower() == 'development':
-        include_interventions = True
+        exclude_interventions = False
 
     # import site export file if found
-    SitePersistence().import_(include_interventions, keep_unmentioned)
+    SitePersistence().import_(exclude_interventions, keep_unmentioned)
 
 
 @app.cli.command()

portal/date_tools.py

@@ -0,0 +1,69 @@
+"""Module for additional datetime tools/utilities"""
+from datetime import date, datetime
+from dateutil import parser
+from flask import abort, current_app
+import pytz
+
+
+def as_fhir(obj):
+    """For builtin types needing FHIR formatting help
+
+    Returns obj as JSON FHIR formatted string
+
+    """
+    if hasattr(obj, 'as_fhir'):
+        return obj.as_fhir()
+    if isinstance(obj, datetime):
+        # Make SURE we only communicate unaware or UTC timezones
+        tz = getattr(obj, 'tzinfo', None)
+        if tz and tz != pytz.utc:
+            current_app.logger.error("Datetime export of NON-UTC timezone")
+        return obj.strftime("%Y-%m-%dT%H:%M:%S%z")
+    if isinstance(obj, date):
+        return obj.strftime('%Y-%m-%d')
+
+
+class FHIR_datetime(object):
+    """Utility class/namespace for working with FHIR datetimes"""
+
+    @staticmethod
+    def as_fhir(obj):
+        return as_fhir(obj)
+
+    @staticmethod
+    def parse(data, error_subject=None):
+        """Parse input string to generate a UTC datetime instance
+
+        NB - date must be more recent than year 1900 or a ValueError
+        will be raised.
+
+        :param data: the datetime string to parse
+        :param error_subject: Subject string to use in error message
+
+        :return: UTC datetime instance from given data
+
+        """
+        # As we use datetime.strftime for display, and it can't handle dates
+        # older than 1900, treat all such dates as an error
+        epoch = datetime.strptime('1900-01-01', '%Y-%m-%d')
+        try:
+            dt = parser.parse(data)
+        except ValueError:
+            msg = "Unable to parse {}: {}".format(error_subject, data)
+            current_app.logger.warn(msg)
+            abort(400, msg)
+        if dt.tzinfo:
+            epoch = pytz.utc.localize(epoch)
+            # Convert to UTC if necessary
+            if dt.tzinfo != pytz.utc:
+                dt = dt.astimezone(pytz.utc)
+        # As we use datetime.strftime for display, and it can't handle dates
+        # older than 1900, treat all such dates as an error
+        if dt < epoch:
+            raise ValueError("Dates prior to year 1900 not supported")
+        return dt
+
+    @staticmethod
+    def now():
+        """Generates a FHIR compliant datetime string for current moment"""
+        return datetime.utcnow().isoformat()+'Z'

portal/migrations/versions/418982ee27e2_.py

@@ -0,0 +1,55 @@
+"""empty message
+
+Revision ID: 418982ee27e2
+Revises: 0ac4b88c909f
+Create Date: 2017-05-02 12:05:13.995805
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = '418982ee27e2'
+down_revision = '0ac4b88c909f'
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('questionnaires',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('name', sa.Text(), nullable=False),
+    sa.Column('document', postgresql.JSONB(astext_type=sa.Text()), nullable=True),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('name')
+    )
+    op.create_table('questionnaire_banks',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('name', sa.Text(), nullable=False),
+    sa.Column('organization_id', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['organization_id'], ['organizations.id'], ),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('name')
+    )
+    op.create_table('questionnaire_bank_questionnaires',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('questionnaire_bank_id', sa.Integer(), nullable=False),
+    sa.Column('questionnaire_id', sa.Integer(), nullable=False),
+    sa.Column('days_till_due', sa.Integer(), nullable=False),
+    sa.Column('days_till_overdue', sa.Integer(), nullable=False),
+    sa.Column('rank', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['questionnaire_bank_id'], ['questionnaire_banks.id'], ondelete='CASCADE'),
+    sa.ForeignKeyConstraint(['questionnaire_id'], ['questionnaires.id'], ondelete='CASCADE'),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('questionnaire_bank_id', 'questionnaire_id', name='_questionnaire_bank_questionnaire'),
+    sa.UniqueConstraint('questionnaire_id', 'rank', name='_questionnaire_bank_questionnaire_rank')
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('questionnaire_bank_questionnaires')
+    op.drop_table('questionnaire_banks')
+    op.drop_table('questionnaires')
+    # ### end Alembic commands ###

portal/migrations/versions/58a9d999ece9_.py

@@ -0,0 +1,34 @@
+"""empty message
+
+Revision ID: 58a9d999ece9
+Revises: 0ac4b88c909f
+Create Date: 2017-04-26 12:39:32.182048
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = '58a9d999ece9'
+down_revision = '0ac4b88c909f'
+
+from alembic import op
+import sqlalchemy as sa
+
+
+def upgrade():
+    ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('organization_locales',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('organization_id', sa.Integer(), nullable=False),
+    sa.Column('coding_id', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['coding_id'], ['codings.id'], ),
+    sa.ForeignKeyConstraint(['organization_id'], ['organizations.id'], ondelete='CASCADE'),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('organization_id', 'coding_id', name='_organization_locale_coding')
+    )
+    ### end Alembic commands ###
+
+
+def downgrade():
+    ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('organization_locales')
+    ### end Alembic commands ###

portal/migrations/versions/5d1daa0f3a14_.py

@@ -0,0 +1,22 @@
+"""empty message
+
+Revision ID: 5d1daa0f3a14
+Revises: ('58a9d999ece9', '418982ee27e2')
+Create Date: 2017-05-03 16:50:12.498677
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = '5d1daa0f3a14'
+down_revision = ('58a9d999ece9', '418982ee27e2')
+
+from alembic import op
+import sqlalchemy as sa
+
+
+def upgrade():
+    pass
+
+
+def downgrade():
+    pass