Merge pull request #96 from ehenneken/db_update

alembic update
adsabs · Feb 10, 2021 · fd8975d · fd8975d
2 parents 8216bb5 + 55edae0
commit fd8975d
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Showing 12 changed files with 188 additions and 43 deletions.
diff --git a/migrations/alembic.ini → alembic.ini b/migrations/alembic.ini → alembic.ini
@@ -1,13 +1,35 @@
 # A generic, single database configuration.
 
 [alembic]
+# path to migration scripts
+script_location = alembic
+
 # template used to generate migration files
 # file_template = %%(rev)s_%%(slug)s
 
+# max length of characters to apply to the
+# "slug" field
+#truncate_slug_length = 40
+
 # set to 'true' to run the environment during
 # the 'revision' command, regardless of autogenerate
 # revision_environment = false
 
+# set to 'true' to allow .pyc and .pyo files without
+# a source .py file to be detected as revisions in the
+# versions/ directory
+# sourceless = false
+
+# set to 'true' to overwrite sqlalchemy.url with value
+# SQLALCHEMY_DATABASE_URI (read from flask application config)
+
+use_flask_db_url = true
+
+# sqlalchemy.url = driver://user:pass@localhost/dbname
+sqlalchemy.url = 'intentionally wrong'
+
+sqlalchemy.echo = False
+
 
 # Logging configuration
 [loggers]

diff --git a/migrations/README → alembic/README b/migrations/README → alembic/README
diff --git a/migrations/env.py → alembic/env.py b/migrations/env.py → alembic/env.py
@@ -2,6 +2,8 @@
 from alembic import context
 from sqlalchemy import engine_from_config, pool
 from logging.config import fileConfig
+import os
+import sys
 
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.
@@ -15,16 +17,18 @@
 # for 'autogenerate' support
 # from myapp import mymodel
 # target_metadata = mymodel.Base.metadata
-from flask import current_app
-config.set_main_option('sqlalchemy.url', current_app.config.get('SQLALCHEMY_DATABASE_URI'))
-target_metadata = current_app.extensions['migrate'].db.metadata
+#target_metadata = None
+opath = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
+if opath not in sys.path:
+    sys.path.insert(0, opath)
+import graphics_service.models
+target_metadata = graphics_service.models.Base.metadata
 
 # other values from the config, defined by the needs of env.py,
 # can be acquired:
 # my_important_option = config.get_main_option("my_important_option")
 # ... etc.
 
-
 def run_migrations_offline():
     """Run migrations in 'offline' mode.
 
@@ -38,11 +42,22 @@ def run_migrations_offline():
 
     """
     url = config.get_main_option("sqlalchemy.url")
-    context.configure(url=url)
+    context.configure(url=url, target_metadata=target_metadata)
 
     with context.begin_transaction():
         context.run_migrations()
 
+def get_app_config(key):
+    opath = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
+    if opath not in sys.path:
+        sys.path.insert(0, opath)
+
+    from graphics_service import app as application
+    app = application.create_app()
+
+    with app.app_context() as c:
+        print('Getting actual config for', key, app.config.get(key))
+        return app.config.get(key)
 
 def run_migrations_online():
     """Run migrations in 'online' mode.
@@ -51,14 +66,21 @@ def run_migrations_online():
     and associate a connection with the context.
 
     """
-    engine = engine_from_config(config.get_section(config.config_ini_section),
-                                prefix='sqlalchemy.',
-                                poolclass=pool.NullPool)
+    cfg = config.get_section(config.config_ini_section)
+    if 'use_flask_db_url' in cfg and cfg['use_flask_db_url'] == 'true':
+        cfg['sqlalchemy.url'] = get_app_config('SQLALCHEMY_DATABASE_URI')
+
+
+    engine = engine_from_config(
+                cfg,
+                prefix='sqlalchemy.',
+                poolclass=pool.NullPool)
 
     connection = engine.connect()
-    context.configure(connection=connection,
-                      target_metadata=target_metadata,
-                      **current_app.extensions['migrate'].configure_args)
+    context.configure(
+                connection=connection,
+                target_metadata=target_metadata
+                )
 
     try:
         with context.begin_transaction():

diff --git a/migrations/script.py.mako → alembic/script.py.mako b/migrations/script.py.mako → alembic/script.py.mako
@@ -1,18 +1,20 @@
 """${message}
 
 Revision ID: ${up_revision}
-Revises: ${down_revision}
+Revises: ${down_revision | comma,n}
 Create Date: ${create_date}
 
 """
+from alembic import op
+import sqlalchemy as sa
+${imports if imports else ""}
 
 # revision identifiers, used by Alembic.
 revision = ${repr(up_revision)}
 down_revision = ${repr(down_revision)}
+branch_labels = ${repr(branch_labels)}
+depends_on = ${repr(depends_on)}
 
-from alembic import op
-import sqlalchemy as sa
-${imports if imports else ""}
 
 def upgrade():
     ${upgrades if upgrades else "pass"}

diff --git a/alembic/versions/437251c0dc94_empty_init.py b/alembic/versions/437251c0dc94_empty_init.py
@@ -0,0 +1,24 @@
+"""Empty init
+
+Revision ID: 437251c0dc94
+Revises:
+Create Date: 2021-02-05 15:14:10.889359
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '437251c0dc94'
+down_revision = None
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    pass
+
+
+def downgrade():
+    pass
diff --git a/alembic/versions/80ecdb88cee2_add_thumbnails_column.py b/alembic/versions/80ecdb88cee2_add_thumbnails_column.py
@@ -0,0 +1,28 @@
+"""Add thumbnails column
+
+Revision ID: 80ecdb88cee2
+Revises: b9308d306405
+Create Date: 2021-02-05 16:32:50.041223
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = '80ecdb88cee2'
+down_revision = 'b9308d306405'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('graphics', sa.Column('thumbnails', postgresql.ARRAY(sa.String()), nullable=True))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column('graphics', 'thumbnails')
+    # ### end Alembic commands ###
diff --git a/alembic/versions/b9308d306405_create_db_tables.py b/alembic/versions/b9308d306405_create_db_tables.py
@@ -0,0 +1,39 @@
+"""Create db tables
+
+Revision ID: b9308d306405
+Revises: 437251c0dc94
+Create Date: 2021-02-05 15:18:06.547834
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = 'b9308d306405'
+down_revision = '437251c0dc94'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('graphics',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('bibcode', sa.String(), nullable=False),
+    sa.Column('doi', sa.String(), nullable=True),
+    sa.Column('source', sa.String(), nullable=True),
+    sa.Column('eprint', sa.Boolean(), nullable=True),
+    sa.Column('figures', postgresql.JSON(astext_type=sa.Text()), nullable=True),
+    sa.Column('modtime', sa.DateTime(), nullable=True),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_graphics_bibcode'), 'graphics', ['bibcode'], unique=False)
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(op.f('ix_graphics_bibcode'), table_name='graphics')
+    op.drop_table('graphics')
+    # ### end Alembic commands ###
diff --git a/alembic/versions/de7cb4b6482f_add_baseurl_column.py b/alembic/versions/de7cb4b6482f_add_baseurl_column.py
@@ -0,0 +1,28 @@
+"""Add baseurl column
+
+Revision ID: de7cb4b6482f
+Revises: 80ecdb88cee2
+Create Date: 2021-02-09 12:36:02.897204
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'de7cb4b6482f'
+down_revision = '80ecdb88cee2'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('graphics', sa.Column('baseurl', sa.String(), nullable=True))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column('graphics', 'baseurl')
+    # ### end Alembic commands ###
diff --git a/graphics_service/models.py b/graphics_service/models.py
@@ -45,6 +45,8 @@ class GraphicsModel(Base):
     source = Column(String)
     eprint = Column(Boolean)
     figures = Column(postgresql.JSON)
+    thumbnails = Column(postgresql.ARRAY(String), default=[])
+    baseurl = Column(String)
     modtime = Column(DateTime)
 
 def execute_SQL_query(bibc):

diff --git a/graphics_service/tests/test_endpoint.py b/graphics_service/tests/test_endpoint.py
@@ -55,10 +55,12 @@ def test_data_model(self):
         sc = Column(String)
         bc = Column(Boolean)
         jc = Column(postgresql.JSON)
+        tc = Column(postgresql.ARRAY(String))
+        uc = Column(String)
         dc = Column(DateTime)
         cols_expect = list(map(
             type, [ic.type, sc.type, sc.type, sc.type, bc.type,
-                   jc.type, dc.type]))
+                   jc.type, tc.type, uc.type, dc.type]))
         self.assertEqual([type(c.type)
                           for c in GraphicsModel.__table__.columns],
                          cols_expect)

diff --git a/graphics_service/tests/test_internals.py b/graphics_service/tests/test_internals.py
@@ -52,7 +52,9 @@ def test_json_encoder(self):
                 modtime=datetime.now()
             )
         results = json.loads(json.dumps(g, cls=AlchemyEncoder))
-        expected = {'modtime': None, 'bibcode': 'bibcode', 'source': 'TEST', 'doi': 'DOI', 'figures': [], 'eprint': False, 'id': None} 
+        expected = {'modtime': None, 'bibcode': 'bibcode', 'thumbnails': None,
+                    'baseurl': None, 'source': 'TEST', 'doi': 'DOI', 'figures': [],
+                    'eprint': False, 'id': None}
         self.assertTrue(results==expected)
 
 class TestLocalConfig(TestCase):

diff --git a/migrations/versions/437251c0dc94_.py b/migrations/versions/437251c0dc94_.py