Merge pull request #878 from MolSSI/create_view

Dataset internal jobs, external files, & server-side view creation

qcarchivetesting/qcarchivetesting/testing_classes.py

@@ -4,13 +4,14 @@
 from copy import deepcopy
 
 from qcarchivetesting import geoip_path, geoip_filename, ip_tests_enabled
-from qcfractal.config import DatabaseConfig, update_nested_dict
+from qcfractal.config import DatabaseConfig
 from qcfractal.db_socket import SQLAlchemySocket
 from qcfractal.postgres_harness import PostgresHarness, create_snowflake_postgres
 from qcfractal.snowflake import FractalSnowflake
 from qcportal import PortalClient, ManagerClient
 from qcportal.auth import UserInfo, GroupInfo
 from qcportal.managers import ManagerName
+from qcportal.utils import update_nested_dict
 from .helpers import test_users, test_groups
 
 _activated_manager_programs = {
@@ -100,7 +101,6 @@ def __init__(
         self,
         pg_harness: QCATestingPostgresHarness,
         encoding: str,
-        start_api=True,
         create_users=False,
         enable_security=False,
         allow_unauthenticated_read=False,
@@ -171,9 +171,7 @@ def __init__(
         if create_users:
             self.create_users()
 
-        # Start the flask api process if requested
-        if start_api:
-            self.start_api()
+        self.start_api()
 
     def create_users(self):
         # Get a storage socket and add the roles/users/passwords

qcarchivetesting/qcarchivetesting/testing_fixtures.py

@@ -13,10 +13,36 @@
 from qcfractal.db_socket.socket import SQLAlchemySocket
 from qcportal import PortalClient
 from qcportal.managers import ManagerName
+from qcportal.utils import update_nested_dict
 from .helpers import geoip_path, geoip_filename, ip_tests_enabled, test_users
 from .testing_classes import QCATestingPostgresServer, QCATestingSnowflake, _activated_manager_programs
 
 
+def _generate_default_config(pg_harness, extra_config=None) -> FractalConfig:
+    # Create a configuration. Since this is mostly just for a storage socket,
+    # We can use defaults for almost all, since a flask server, etc, won't be instantiated
+    # Also disable connection pooling in the storage socket
+    # (which can leave db connections open, causing problems when we go to delete
+    # the database)
+    cfg_dict = {}
+    cfg_dict["base_folder"] = pg_harness.config.base_folder
+    cfg_dict["loglevel"] = "DEBUG"
+    cfg_dict["database"] = pg_harness.config.dict()
+    cfg_dict["database"]["pool_size"] = 0
+    cfg_dict["log_access"] = True
+
+    if ip_tests_enabled:
+        cfg_dict["geoip2_dir"] = geoip_path
+        cfg_dict["geoip2_filename"] = geoip_filename
+
+    cfg_dict["api"] = {"secret_key": secrets.token_urlsafe(32), "jwt_secret_key": secrets.token_urlsafe(32)}
+
+    if extra_config:
+        cfg_dict = update_nested_dict(cfg_dict, extra_config)
+
+    return FractalConfig(**cfg_dict)
+
+
 @pytest.fixture(scope="session")
 def postgres_server(tmp_path_factory):
     """
@@ -40,26 +66,7 @@ def session_storage_socket(postgres_server):
     """
 
     pg_harness = postgres_server.get_new_harness("session_storage")
-
-    # Create a configuration. Since this is mostly just for a storage socket,
-    # We can use defaults for almost all, since a flask server, etc, won't be instantiated
-    # Also disable connection pooling in the storage socket
-    # (which can leave db connections open, causing problems when we go to delete
-    # the database)
-    cfg_dict = {}
-    cfg_dict["base_folder"] = pg_harness.config.base_folder
-    cfg_dict["loglevel"] = "DEBUG"
-    cfg_dict["database"] = pg_harness.config.dict()
-    cfg_dict["database"]["pool_size"] = 0
-    cfg_dict["log_access"] = True
-
-    if ip_tests_enabled:
-        cfg_dict["geoip2_dir"] = geoip_path
-        cfg_dict["geoip2_filename"] = geoip_filename
-
-    cfg_dict["api"] = {"secret_key": secrets.token_urlsafe(32), "jwt_secret_key": secrets.token_urlsafe(32)}
-    qcf_config = FractalConfig(**cfg_dict)
-
+    qcf_config = _generate_default_config(pg_harness)
     socket = SQLAlchemySocket(qcf_config)
 
     # Create the template database for use in re-creating the database

qcfractal/pyproject.toml

@@ -42,6 +42,9 @@ geoip = [
 snowflake = [
     "qcfractalcompute"
 ]
+s3 = [
+    "boto3"
+]
 
 
 [project.urls]

qcfractal/qcfractal/alembic/versions/2025-01-02-e798462e0c03_add_repeat_delay_to_internal_jobs.py

@@ -20,6 +20,19 @@
 def upgrade():
     # ### commands auto generated by Alembic - please adjust! ###
     op.add_column("internal_jobs", sa.Column("repeat_delay", sa.Integer(), nullable=True))
+
+    # Remove old periodic tasks
+    op.execute(
+        """DELETE FROM internal_jobs WHERE status IN ('waiting', 'running') AND name IN (
+                       'delete_old_internal_jobs',
+                       'delete_old_access_log',
+                       'iterate_services',
+                       'geolocate_accesses',
+                       'check_manager_heartbeats',
+                       'update_geoip2_file'
+                  )
+               """
+    )
     # ### end Alembic commands ###
 
 

qcfractal/qcfractal/alembic/versions/2025-01-03-02afa97249c7_add_external_files_table.py

@@ -0,0 +1,43 @@
+"""Add external files table
+
+Revision ID: 02afa97249c7
+Revises: c13116948b54
+Create Date: 2025-01-03 10:01:55.717905
+
+"""
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = "02afa97249c7"
+down_revision = "c13116948b54"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "external_file",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("created_on", sa.TIMESTAMP(), nullable=False),
+        sa.Column("status", sa.Enum("available", "processing", name="externalfilestatusenum"), nullable=False),
+        sa.Column("file_type", sa.Enum("dataset_attachment", name="externalfiletypeenum"), nullable=False),
+        sa.Column("bucket", sa.String(), nullable=False),
+        sa.Column("file_name", sa.String(), nullable=False),
+        sa.Column("object_key", sa.String(), nullable=False),
+        sa.Column("sha256sum", sa.String(), nullable=False),
+        sa.Column("file_size", sa.BigInteger(), nullable=False),
+        sa.Column("description", sa.String(), nullable=True),
+        sa.Column("provenance", postgresql.JSONB(astext_type=sa.Text()), nullable=False),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table("external_file")
+    # ### end Alembic commands ###

qcfractal/qcfractal/alembic/versions/2025-01-03-84285e3620fd_add_dataset_attachment_table.py

@@ -0,0 +1,38 @@
+"""Add dataset attachment table
+
+Revision ID: 84285e3620fd
+Revises: 02afa97249c7
+Create Date: 2025-01-03 10:04:16.201770
+
+"""
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "84285e3620fd"
+down_revision = "02afa97249c7"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "dataset_attachment",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("dataset_id", sa.Integer(), nullable=False),
+        sa.Column("attachment_type", sa.Enum("other", "view", name="datasetattachmenttype"), nullable=False),
+        sa.ForeignKeyConstraint(["dataset_id"], ["base_dataset.id"], ondelete="cascade"),
+        sa.ForeignKeyConstraint(["id"], ["external_file.id"], ondelete="cascade"),
+        sa.PrimaryKeyConstraint("id"),
+    )
+    op.create_index("ix_dataset_attachment_dataset_id", "dataset_attachment", ["dataset_id"], unique=False)
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index("ix_dataset_attachment_dataset_id", table_name="dataset_attachment")
+    op.drop_table("dataset_attachment")
+    # ### end Alembic commands ###

qcfractal/qcfractal/alembic/versions/2025-01-07-c13116948b54_add_progress_description.py

@@ -0,0 +1,28 @@
+"""Add progress description
+
+Revision ID: c13116948b54
+Revises: e798462e0c03
+Create Date: 2025-01-07 10:35:23.654928
+
+"""
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "c13116948b54"
+down_revision = "e798462e0c03"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column("internal_jobs", sa.Column("progress_description", sa.String(), nullable=True))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column("internal_jobs", "progress_description")
+    # ### end Alembic commands ###

qcfractal/qcfractal/alembic/versions/2025-01-09-5f6f804e11d3_add_dataset_internal_jobs.py

@@ -0,0 +1,35 @@
+"""Add dataset internal jobs
+
+Revision ID: 5f6f804e11d3
+Revises: 84285e3620fd
+Create Date: 2025-01-09 16:25:50.187495
+
+"""
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "5f6f804e11d3"
+down_revision = "84285e3620fd"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "dataset_internal_job",
+        sa.Column("internal_job_id", sa.Integer(), nullable=False),
+        sa.Column("dataset_id", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(["dataset_id"], ["base_dataset.id"], ondelete="cascade"),
+        sa.ForeignKeyConstraint(["internal_job_id"], ["internal_jobs.id"], ondelete="cascade"),
+        sa.PrimaryKeyConstraint("internal_job_id", "dataset_id"),
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table("dataset_internal_job")
+    # ### end Alembic commands ###

qcfractal/qcfractal/alembic/versions/2025-01-10-3690c677f8d1_add_internal_job_serial_group.py

@@ -0,0 +1,40 @@
+"""Add internal job serial group
+
+Revision ID: 3690c677f8d1
+Revises: 5f6f804e11d3
+Create Date: 2025-01-10 16:08:36.541807
+
+"""
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "3690c677f8d1"
+down_revision = "5f6f804e11d3"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column("internal_jobs", sa.Column("serial_group", sa.String(), nullable=True))
+    op.create_index(
+        "ux_internal_jobs_status_serial_group",
+        "internal_jobs",
+        ["status", "serial_group"],
+        unique=True,
+        postgresql_where=sa.text("status = 'running'"),
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(
+        "ux_internal_jobs_status_serial_group",
+        table_name="internal_jobs",
+        postgresql_where=sa.text("status = 'running'"),
+    )
+    op.drop_column("internal_jobs", "serial_group")
+    # ### end Alembic commands ###

qcfractal/qcfractal/components/auth/test_auth_permissions.py

@@ -19,7 +19,6 @@ def module_authtest_snowflake(postgres_server, pytestconfig):
     with QCATestingSnowflake(
         pg_harness,
         encoding,
-        start_api=True,
         create_users=False,
         enable_security=True,
         allow_unauthenticated_read=False,