feat: optional keep 'created' time column

materializationengine/config.py

@@ -48,7 +48,7 @@ class BaseConfig:
             AUTH_TOKEN = json.load(f)["token"]
     else:
         AUTH_TOKEN = ""
-
+    KEEP_CREATED_COLUMN = False
     BEAT_SCHEDULES = [
         {
             "name": "Materialized Database Daily (2 Days)",

materializationengine/models.py

@@ -1,4 +1,4 @@
-from sqlalchemy import Column, String, Integer, DateTime
+from sqlalchemy import Column, String, Integer, DateTime, Boolean
 from sqlalchemy.ext.declarative import declarative_base
 
 MatBase = declarative_base()
@@ -11,3 +11,6 @@ class MaterializedMetadata(MatBase):
     table_name = Column(String(100), nullable=False)
     row_count = Column(Integer, nullable=False)
     materialized_timestamp = Column(DateTime, nullable=False)
+    segmentation_source = Column(String(255), nullable=True)
+    is_merged = Column(Boolean, nullable=True)
+    has_created_ts = Column(Boolean, nullable=True)

materializationengine/shared_tasks.py

@@ -196,6 +196,7 @@ def get_materialization_info(
                 "reference_table": reference_table,
                 "materialization_time_stamp": str(materialization_time_stamp),
                 "table_count": len(annotation_tables),
+                "keep_created_ts_col": md.get("keep_created_ts_col", False)
             }
             has_segmentation_table = db.schema.is_segmentation_table_required(schema)
             if has_segmentation_table:

materializationengine/views.py

@@ -11,7 +11,6 @@
     AnalysisVersion,
     VersionErrorTable,
     AnnoMetadata,
-    MaterializedMetadata,
 )
 from dynamicannotationdb.schema import DynamicSchemaClient
 from flask import (
@@ -32,6 +31,7 @@
 from materializationengine.celery_init import celery
 from materializationengine.blueprints.client.query import specific_query
 from materializationengine.database import sqlalchemy_cache, dynamic_annotation_cache
+from materializationengine.models import MaterializedMetadata
 from materializationengine.info_client import (
     get_datastack_info,
     get_datastacks,

materializationengine/workflows/create_frozen_database.py

@@ -12,7 +12,6 @@
     AnalysisVersion,
     AnnoMetadata,
     Base,
-    MaterializedMetadata,
 )
 from emannotationschemas import get_schema
 from emannotationschemas.flatten import create_flattened_schema
@@ -28,6 +27,7 @@
     dynamic_annotation_cache,
     sqlalchemy_cache,
 )
+from materializationengine.models import MaterializedMetadata
 from materializationengine.errors import IndexMatchError
 from materializationengine.index_manager import index_cache
 from materializationengine.shared_tasks import (
@@ -403,7 +403,8 @@ def create_materialized_metadata(
             valid_row_count = mat_metadata["row_count"]
             segmentation_source = mat_metadata.get("segmentation_source")
             merge_table = mat_metadata.get("merge_table")
-
+            has_created_ts = mat_metadata.get("keep_created_ts_col")
+
             celery_logger.info(f"Row count {valid_row_count}")
             if valid_row_count == 0:
                 continue
@@ -415,6 +416,7 @@ def create_materialized_metadata(
                 materialized_timestamp=materialization_time_stamp,
                 segmentation_source=segmentation_source,
                 is_merged=merge_table,
+                has_created_ts=has_created_ts
             )
             analysis_session.add(mat_metadata)
             analysis_session.commit()
@@ -651,7 +653,12 @@ def merge_tables(self, mat_metadata: dict):
         mat_metadata, with_crud_columns=True
     )
     SegmentationModel = create_segmentation_model(mat_metadata)
-    crud_columns = ["created", "deleted", "superceded_id"]
+
+    keep_created = mat_metadata.get("keep_created_ts_col")
+    crud_columns = ["created", "deleted", "superceded_id"] # crud cols to drop
+    if keep_created:
+        crud_columns.pop(0) # we want to keep the 'created' col
+
     query_columns = {
         col.name: col
         for col in AnnotationModel.__table__.columns

migration/alembic.ini

@@ -0,0 +1,102 @@
+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+script_location = .
+
+# template used to generate migration files
+# file_template = %%(rev)s_%%(slug)s
+
+# sys.path path, will be prepended to sys.path if present.
+# defaults to the current working directory.
+prepend_sys_path = .
+
+# timezone to use when rendering the date within the migration file
+# as well as the filename.
+# If specified, requires the python-dateutil library that can be
+# installed by adding `alembic[tz]` to the pip requirements
+# string value is passed to dateutil.tz.gettz()
+# leave blank for localtime
+# timezone =
+
+# 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
+
+# version location specification; This defaults
+# to migration/versions.  When using multiple version
+# directories, initial revisions must be specified with --version-path.
+# The path separator used here should be the separator specified by "version_path_separator" below.
+# version_locations = %(here)s/bar:%(here)s/bat:migration/versions
+
+# version path separator; As mentioned above, this is the character used to split
+# version_locations. The default within new alembic.ini files is "os", which uses os.pathsep.
+# If this key is omitted entirely, it falls back to the legacy behavior of splitting on spaces and/or commas.
+# Valid values for version_path_separator are:
+#
+# version_path_separator = :
+# version_path_separator = ;
+# version_path_separator = space
+version_path_separator = os  # Use os.pathsep. Default configuration used for new projects.
+
+# the output encoding used when revision files
+# are written from script.py.mako
+# output_encoding = utf-8
+
+# sqlalchemy.url = 
+
+
+[post_write_hooks]
+# post_write_hooks defines scripts or Python functions that are run
+# on newly generated revision scripts.  See the documentation for further
+# detail and examples
+
+# format using "black" - use the console_scripts runner, against the "black" entrypoint
+# hooks = black
+# black.type = console_scripts
+# black.entrypoint = black
+# black.options = -l 79 REVISION_SCRIPT_FILENAME
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

migration/env.py

@@ -0,0 +1,75 @@
+from logging.config import fileConfig
+
+from sqlalchemy import engine_from_config
+from sqlalchemy import pool
+
+from alembic import context
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+fileConfig(config.config_file_name)
+
+# add your model's MetaData object here
+from materializationengine.models import MatBase
+target_metadata = MatBase.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.
+
+    This configures the context with just a URL
+    and not an Engine, though an Engine is acceptable
+    here as well.  By skipping the Engine creation
+    we don't even need a DBAPI to be available.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        dialect_opts={"paramstyle": "named"},
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def run_migrations_online():
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+    connectable = engine_from_config(
+        config.get_section(config.config_ini_section),
+        prefix="sqlalchemy.",
+        poolclass=pool.NullPool,
+    )
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection, target_metadata=target_metadata
+        )
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()

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"}

migration/versions/4006a7c94f25_add_has_timestamp_col.py

@@ -0,0 +1,27 @@
+"""Add has timestamp col
+
+Revision ID: 4006a7c94f25
+Revises: 8ff84a0bb8f8
+Create Date: 2023-01-03 10:53:44.569973
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = "4006a7c94f25"
+down_revision = "8ff84a0bb8f8"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    op.add_column(
+        "materializedmetadata", sa.Column("has_created_ts", sa.Boolean(), nullable=True)
+    )
+    op.execute("UPDATE materializedmetadata SET has_created_ts = False")
+
+
+def downgrade():
+    op.drop_column("materializedmetadata", "has_created_ts")

migration/versions/8ff84a0bb8f8_base_mat_metadata.py

@@ -0,0 +1,46 @@
+"""Base mat metadata
+
+Revision ID: 8ff84a0bb8f8
+Revises: 
+Create Date: 2023-01-03 10:50:35.866055
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.engine import reflection
+from sqlalchemy import engine_from_config
+
+# revision identifiers, used by Alembic.
+revision = "8ff84a0bb8f8"
+down_revision = None
+branch_labels = None
+depends_on = None
+
+
+def get_tables():
+    config = op.get_context().config
+    engine = engine_from_config(
+        config.get_section(config.config_ini_section), prefix="sqlalchemy."
+    )
+    inspector = reflection.Inspector.from_engine(engine)
+    return inspector.get_table_names()
+
+
+def upgrade():
+    tables = get_tables()
+    if "materializedmetadata" not in tables:
+        op.create_table(
+            "materializedmetadata",
+            sa.Column("id", sa.Integer(), nullable=False),
+            sa.Column("schema", sa.String(length=100), nullable=False),
+            sa.Column("table_name", sa.String(length=100), nullable=False),
+            sa.Column("row_count", sa.Integer(), nullable=False),
+            sa.Column("materialized_timestamp", sa.DateTime(), nullable=False),
+            sa.Column("segmentation_source", sa.String(length=255), nullable=True),
+            sa.Column("is_merged", sa.Boolean(), nullable=True),
+            sa.PrimaryKeyConstraint("id"),
+        )
+
+
+def downgrade():
+    op.drop_table("materializedmetadata")

tests/test_shared_tasks.py

@@ -63,6 +63,7 @@ def test_get_materialization_info(self):
                 "chunk_size": 2,
                 "table_count": 1,
                 "find_all_expired_roots": False,
+                'keep_created_ts_col': False,
                 "analysis_version": 1,
                 "analysis_database": "test_datastack__mat1",
                 "queue_length_limit": 10000,