Merge pull request #32 from Caleydo/release-2.0.1

Release 2.0.1

coral/__init__.py

@@ -3,6 +3,10 @@
 # Copyright (c) The Caleydo Team. All rights reserved.
 # Licensed under the new BSD license, available at http://caleydo.org/license
 ###############################################################################
+from os import path
+
+PROJ_NAME = 'coral'
+DB_KEY = 'cohortdb'
 
 
 def phovea(registry):
@@ -11,14 +15,22 @@ def phovea(registry):
   :param registry:
   """
   # generator-phovea:begin
-  registry.append('tdp-sql-database-definition', 'cohortdb', 'coral.db', {
-     'configKey': 'coral'
+  registry.append('tdp-sql-database-definition', DB_KEY, f'{PROJ_NAME}.db', {
+     'configKey': f'{PROJ_NAME}'
     })
 
-  registry.append('namespace', 'db_connector', 'coral.sql', {
+  registry.append('namespace', 'db_connector', f'{PROJ_NAME}.sql', {
        'namespace': '/api/cohortdb/db'
     })
   # generator-phovea:end
+
+  registry.append('tdp-sql-database-migration', DB_KEY, '', {
+    'scriptLocation': path.join(path.abspath(path.dirname(__file__)), 'migration'),
+    'configKey': f'{PROJ_NAME}.migration',
+    'dbKey': DB_KEY,
+    'versionTableSchema': 'public'
+  })
+
   pass
 
 

coral/migration/README

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

coral/migration/env.py

@@ -0,0 +1,3 @@
+import tdp_core.dbmigration_env  # NOQA
+
+tdp_core.dbmigration_env.run_migrations_online()

coral/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"}

coral/migration/versions/20220414_1158_ddd776aa28c3_.py

@@ -0,0 +1,46 @@
+"""Create cohort schema, sequence and table
+
+Revision ID: ddd776aa28c3
+Revises:
+Create Date: 2022-04-14 11:58:27.444788
+
+"""
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = 'ddd776aa28c3'
+down_revision = None
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    connection = op.get_bind()
+    for cmd in ["""
+CREATE SCHEMA IF NOT EXISTS cohort;
+CREATE SEQUENCE cohort.cohort_id_seq
+    INCREMENT 1
+    START 1
+    MINVALUE 1
+    MAXVALUE 2147483647
+    CACHE 1;
+""", """
+CREATE TABLE cohort.cohort
+(
+    id integer NOT NULL DEFAULT nextval('cohort.cohort_id_seq'::regclass),
+    name character varying COLLATE pg_catalog."default" NOT NULL,
+    is_initial integer NOT NULL,
+    previous_cohort integer,
+    entity_database character varying COLLATE pg_catalog."default" NOT NULL,
+    entity_schema character varying COLLATE pg_catalog."default" NOT NULL,
+    entity_table character varying COLLATE pg_catalog."default" NOT NULL,
+    statement character varying COLLATE pg_catalog."default",
+    CONSTRAINT cohort_pkey PRIMARY KEY (id)
+);
+"""]:
+        connection.execute(cmd)
+
+
+def downgrade():
+    connection = op.get_bind()
+    connection.execute("DROP SCHEMA cohort CASCADE;")

package.json

@@ -2,7 +2,7 @@
   "name": "coral",
   "description": "Coral is a web-based cohort analysis tool to interactively create, refine, and analyze patient cohorts.",
   "homepage": "https://caleydo.org",
-  "version": "2.0.0",
+  "version": "2.0.1",
   "author": {
     "name": "PatrickAdelberger",
     "email": "coral@caleydo.org",
@@ -99,7 +99,7 @@
     "react-dom": "^16.13.0",
     "react-router-dom": "^5.2.0",
     "split-grid": "^1.0.9",
-    "tdp_publicdb": "github:caleydo/tdp_publicdb#develop",
+    "tdp_publicdb": "github:caleydo/tdp_publicdb#semver:^11.0.0",
     "tippy.js": "^6.2.6",
     "tourdino": "github:caleydo/tourdino#keckelt/vega_boxplot",
     "vega": "~5.20.0",

requirements.txt

@@ -1,2 +1,2 @@
--e git+https://github.com/phovea/phovea_server.git@develop#egg=phovea_server
--e git+https://github.com/datavisyn/tdp_core.git@develop#egg=tdp_core
+phovea_server>=9.0.0,<10.0.0
+tdp_core>=14.0.2,<15.0.0