Integrate alembic and add hg38 DB schema as initial revision

package.json

@@ -66,7 +66,13 @@
     "build:web": "webpack --env prod",
     "predist:python": "npm run build:python && npm run docs:python",
     "prebuild:python": "node -e \"process.exit(process.env.PHOVEA_SKIP_TESTS === undefined?1:0)\" || npm run test:python",
-    "prebuild:web": "node -e \"process.exit(process.env.PHOVEA_SKIP_TESTS === undefined?1:0)\" || npm run test:web"
+    "prebuild:web": "node -e \"process.exit(process.env.PHOVEA_SKIP_TESTS === undefined?1:0)\" || npm run test:web",
+    "db-migration": "cd ../tdp_core && npm run db-migration -- tdp_publicdb",
+    "db-migration:upgrade": "npm run db-migration -- upgrade",
+    "db-migration:upgrade:head": "npm run db-migration -- upgrade head",
+    "db-migration:downgrade": "npm run db-migration -- downgrade",
+    "db-migration:current": "npm run db-migration -- current",
+    "db-migration:history": "npm run db-migration -- history"
   },
   "main": "build/tdp_publicdb.js",
   "engines": {

requirements.txt

@@ -1,2 +1,2 @@
--e git+https://github.com/datavisyn/tdp_core.git@develop#egg=tdp_core
+-e git+https://github.com/datavisyn/tdp_core.git@mp/291_db_migration#egg=tdp_core
 psycopg2==2.8.3

tdp_publicdb/__init__.py

@@ -12,6 +12,13 @@ def phovea(registry):
   """
   # generator-phovea:begin
   registry.append('tdp-sql-database-definition', 'publicdb', 'tdp_publicdb.sql', dict(configKey='tdp_publicdb'))
+
+  from os import path
+  registry.append('tdp-sql-database-migration', 'tdp_publicdb', '', {
+    'scriptLocation': path.join(path.abspath(path.dirname(__file__)), 'migration'),
+    'configKey': 'tdp_publicdb.migration',
+    'dbKey': 'publicdb'
+  })
   # generator-phovea:end
   pass
 

tdp_publicdb/migration/README

@@ -0,0 +1 @@
+Generic single-database configuration.

tdp_publicdb/migration/env.py

@@ -0,0 +1 @@
+import tdp_core.dbmigration_env  # NOQA

tdp_publicdb/migration/script.py.mako

@@ -0,0 +1,24 @@
+"""${message}
+
+Revision ID: ${up_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)}
+
+
+def upgrade():
+    ${upgrades if upgrades else "pass"}
+
+
+def downgrade():
+    ${downgrades if downgrades else "pass"}

tdp_publicdb/migration/versions/20200302_1312_b477004c3673_First_Revision.py

@@ -0,0 +1,35 @@
+"""First_Revision
+
+Revision ID: b477004c3673
+Revises:
+Create Date: 2020-03-02 13:12:59.636711
+
+"""
+from alembic import op
+from codecs import open
+import sqlalchemy as sa
+from os import path
+
+# revision identifiers, used by Alembic.
+revision = 'b477004c3673'
+down_revision = None
+branch_labels = None
+depends_on = None
+
+# import the schema
+here = path.relpath(path.dirname(__file__))
+sql_file_path = path.join(here, './assets/ordino-schema-postgres12.sql')
+ordino_hg38_schema = open(sql_file_path, mode='r').read()
+
+
+def upgrade():
+    connection = op.get_bind()
+    # escape special characters before executing
+    connection.execute(sa.text(ordino_hg38_schema))
+    pass
+
+
+def downgrade():
+    """
+    """
+    pass