Upgrade/python 3.12

.coveragerc

@@ -1,2 +1,2 @@
 [run]
-omit = vault_service/tests*
+omit = */vault_service/tests/*

.github/workflows/python_actions.yml

@@ -15,7 +15,7 @@ jobs:
 
     services:
       postgres:
-        image: postgres:9.6
+        image: postgres:15
         env:
           POSTGRES_DB: test
           POSTGRES_PASSWORD: postgres
@@ -35,17 +35,15 @@ jobs:
     - uses: actions/checkout@v2
     - uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: '3.12'
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade wheel setuptools==56 pip
-        pip install -U -r requirements.txt
-        pip install -U -r dev-requirements.txt
+        pip install ".[dev]"
 
     - name: Test with pytest
       run: |
-        py.test vault_service
+        pytest
 
     - name: Upload coverage data to coveralls.io
       run: coveralls

README.md

@@ -14,13 +14,22 @@ Microservice for storing queries, user preferences and stuff
      create database vault;
      alter database vault owner to vault;
 
-  * create modified vault_service/local_config.py, update (at least)
+  * create local_config.py at the repo root (next to config.py), update (at least)
   	VAULT_OAUTH_CLIENT_TOKEN = '.......'
     SQLALCHEMY_DATABASE_URI = "....."
 
   * run `alembic upgrade head`
 
-  	* note: you need alembic and all dependencies in your python (`virtualenv python; pip install -r requirements; source python/bin/activate`)
+  	* note: you need alembic and all dependencies in your python
+
+```bash
+python3.12 -m venv python
+source python/bin/activate
+pip install -e ".[dev]"
+
+# run the tests
+pytest
+```
 
 
 

alembic/env.py

@@ -1,4 +1,3 @@
-from __future__ import with_statement
 from alembic import context
 from sqlalchemy import engine_from_config, pool
 from logging.config import fileConfig

alembic/versions/4cc89f2f896b_add_scix_ui_column_with_default_false.py

@@ -14,7 +14,6 @@
 import sqlalchemy as sa
 
 
-from sqlalchemy.dialects import postgresql
 
 def upgrade():
     #with app.app_context() as c:

alembic/versions/717c2970ff42_add_get_other_papers_flag_to_myads_table.py

@@ -14,7 +14,6 @@
 import sqlalchemy as sa
 
 
-from sqlalchemy.dialects import postgresql
 
 def upgrade():
     #with app.app_context() as c:

alembic/versions/af63c0205b19_adding_library_id_foreign_key_to_user.py

@@ -14,7 +14,6 @@
 import sqlalchemy as sa
 import json
 
-from sqlalchemy.dialects import postgresql
 
 def upgrade():
     #with app.app_context() as c:
@@ -31,7 +30,7 @@ def upgrade():
     # Delete link_server from user_data 
     # But save the link_server in the library table instead to be accessible via users.library_id
 
-    users = bind.execute("SELECT id, user_data FROM users WHERE user_data ? 'link_server'")
+    users = bind.execute(sa.text("SELECT id, user_data FROM users WHERE user_data ? 'link_server'"))
 
     for user_id, user_data in users: 
         if user_data and isinstance(user_data, dict): 
@@ -40,7 +39,7 @@ def upgrade():
                 library_id = None
                 if link_server:  # Only look up library if link_server is not empty
                     library_result = bind.execute(
-                        "SELECT id FROM library WHERE libserver = %(libserver)s", 
+                        sa.text("SELECT id FROM library WHERE libserver = :libserver"),
                         {"libserver": link_server}
                     ).fetchone()
                     library_id = library_result[0] if library_result else None
@@ -50,7 +49,7 @@ def upgrade():
 
                 # Convert dictionary to JSON string for PostgreSQL
                 bind.execute(
-                    "UPDATE users SET user_data = %(user_data)s, library_id = %(library_id)s WHERE id = %(user_id)s",
+                    sa.text("UPDATE users SET user_data = :user_data, library_id = :library_id WHERE id = :user_id"),
                     {
                         "user_data": json.dumps(new_user_data),
                         "library_id": library_id, 
@@ -63,15 +62,15 @@ def downgrade():
 
     bind = op.get_bind()
 
-    result = bind.execute("SELECT u.id, u.user_data, l.libserver FROM users u JOIN library l ON u.library_id = l.id WHERE u.library_id IS NOT NULL")
+    result = bind.execute(sa.text("SELECT u.id, u.user_data, l.libserver FROM users u JOIN library l ON u.library_id = l.id WHERE u.library_id IS NOT NULL"))
 
     for user_id, user_data, libserver in result: 
         user_data = user_data or {}
         if isinstance(user_data, dict): 
             if libserver is not None: 
                 user_data['link_server'] = libserver
             bind.execute(
-                "UPDATE users SET user_data = %(user_data)s WHERE id = %(user_id)s", 
+                sa.text("UPDATE users SET user_data = :user_data WHERE id = :user_id"),
                 {
                     "user_data": json.dumps(user_data), 
                     "user_id": user_id
@@ -80,12 +79,12 @@ def downgrade():
 
     # Find and drop the actual foreign key constraint
     bind = op.get_bind()
-    result = bind.execute("""
+    result = bind.execute(sa.text("""
         SELECT constraint_name 
         FROM information_schema.table_constraints 
         WHERE table_name = 'users' 
         AND constraint_type = 'FOREIGN KEY'
-    """).fetchone()
+    """)).fetchone()
 
     if result:
         constraint_name = result[0]

alembic/versions/ffdbd392dc89_myads_nullable_fix.py

@@ -11,7 +11,6 @@
 down_revision = 'c342556e5569'
 
 from alembic import op
-import sqlalchemy as sa
 
 
 

pyproject.toml

@@ -0,0 +1,50 @@
+[project]
+name = "vault_service"
+version = "0.0.1"
+description = "ADS Vault Service"
+authors = [{ name = "ADS Team", email = "adshelp@cfa.harvard.edu" }]
+license = { text = "MIT" }
+readme = "README.md"
+requires-python = ">=3.12"
+dependencies = [
+    "adsmutils @ git+https://github.com/adsabs/ADSMicroserviceUtils.git@v2.0.0",
+    "ADSParser @ git+https://github.com/adsabs/ADSParser.git@v1.0.4",
+    "Flask-Cors==6.0.5",
+    "alembic==1.19.1",
+    "psycopg2-binary==2.9.12",
+    "Jinja2==3.1.6",
+    "markupsafe==3.0.3",
+    "itsdangerous==2.2.0",
+    "werkzeug==2.3.8"
+]
+
+[project.optional-dependencies]
+dev = [
+    "Flask-Testing==0.8.1",
+    "httpretty==1.1.4",
+    "testing.postgresql==1.3.0",
+    "pytest==9.1.1",
+    "pytest-cov==7.1.0",
+    "coverage==7.16.0",
+    "coveralls==4.1.0"
+]
+
+[build-system]
+requires = ["setuptools>=62.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+include = ["vault_service*"]
+exclude = ["vault_service.tests*"]
+
+[tool.pytest.ini_options]
+addopts = "--cov=vault_service --cov-report=term-missing"
+testpaths = ["vault_service/tests"]
+pythonpath = ["."]
+
+[tool.black]
+line-length = 88
+target-version = ['py312']
+
+[tool.isort]
+profile = "black"

vault_service/app.py

@@ -1,4 +1,3 @@
-import logging.config
 
 from werkzeug.serving import run_simple
 import os, sys, inspect
@@ -26,7 +25,7 @@ def create_app(**config):
     ## http://docs.sqlalchemy.org/en/rel_0_9/dialects/sqlite.html#pysqlite-serializable
 
     if 'sqlite' in app.config.get('SQLALCHEMY_DATABASE_URI', None):
-        from sqlalchemy import event
+        from sqlalchemy import event, text
         engine = app.db.engine
 
         @event.listens_for(engine, "connect")
@@ -38,7 +37,7 @@ def do_connect(dbapi_connection, connection_record):
         @event.listens_for(engine, "begin")
         def do_begin(conn):
             # emit our own BEGIN
-            conn.execute("BEGIN")
+            conn.execute(text("BEGIN"))
 
 
     # Note about imports being here rather than at the top level

vault_service/models.py

@@ -7,7 +7,7 @@
 """
 from sqlalchemy import Column, Integer, String, LargeBinary, ForeignKey, Boolean, Text
 from sqlalchemy.dialects.postgresql import JSONB, ENUM, ARRAY
-from sqlalchemy.ext.declarative import declarative_base
+from sqlalchemy.orm import declarative_base
 from sqlalchemy.ext.mutable import MutableDict
 from adsmutils import UTCDateTime, get_date
 import sqlalchemy as sa

vault_service/tests/test_bumblebee.py

@@ -1,15 +1,13 @@
 import sys, os
-from urllib.parse import urlencode
-from flask import url_for, request
+from flask import url_for
 import unittest
-import json
 
 project_home = os.path.abspath(os.path.join(os.path.dirname(__file__), '../../'))
 if project_home not in sys.path:
     sys.path.insert(0, project_home)
 
 from vault_service import app
-from vault_service.models import Query, Institute, Library, Base
+from vault_service.models import Institute, Library, Base
 from vault_service.tests.base import TestCaseDatabase
 
 class TestSite(TestCaseDatabase):

vault_service/tests/test_query_as_monument.py

@@ -1,11 +1,7 @@
 import sys, os
-from urllib.parse import urlencode
-from flask import url_for, request
+from flask import url_for
 import unittest
 import json
-import httpretty
-import cgi
-from io import StringIO
 
 project_home = os.path.abspath(os.path.join(os.path.dirname(__file__), '../../'))
 if project_home not in sys.path:

vault_service/tests/test_service.py

@@ -1,16 +1,10 @@
 import sys, os
-from urllib.parse import urlencode
 
 project_home = os.path.abspath(os.path.join(os.path.dirname(__file__), '../../'))
 if project_home not in sys.path:
     sys.path.insert(0, project_home)
 
-from flask import url_for, request
 import unittest
-import json
-import httpretty
-import cgi
-from io import StringIO
 from vault_service.tests.base import TestCaseDatabase
 
 class TestServices(TestCaseDatabase):

vault_service/tests/test_utils.py

@@ -1,20 +1,16 @@
 import sys, os
-from urllib.parse import urlencode
-from flask import url_for, request
+from flask import url_for
 import unittest
 import json
 import httpretty
-import cgi
-from io import StringIO
 
 project_home = os.path.abspath(os.path.join(os.path.dirname(__file__), '../../'))
 if project_home not in sys.path:
     sys.path.insert(0, project_home)
 
-from vault_service.models import Query, User, MyADS
+from vault_service.models import MyADS
 from vault_service.views import utils
 from vault_service.tests.base import TestCaseDatabase
-import adsmutils
 
 
 class TestServices(TestCaseDatabase):

vault_service/views/user.py

@@ -1,6 +1,6 @@
 from flask import Blueprint
 from flask import current_app
-from flask import request, url_for
+from flask import request
 
 import json
 from hashlib import md5

vault_service/views/utils.py

@@ -9,7 +9,6 @@
 
 from sqlalchemy import exc
 from sqlalchemy.orm import exc as ormexc
-from sqlalchemy.sql.expression import all_
 
 
 def make_solr_request(query, bigquery=None, headers=None):