Refactor Alembic migration scripts and update alembic_check.sh

alembic/versions/74f7f1590fb6_create_rtransparentpublication_tables.py → alembic/versions/52101c205c9d_initial_migration.py

@@ -1,8 +1,8 @@
-"""Create RTransparentPublication tables
+"""initial migration
 
-Revision ID: 74f7f1590fb6
-Revises: 4a908d10b459
-Create Date: 2024-11-29 16:32:06.283873
+Revision ID: 52101c205c9d
+Revises: 
+Create Date: 2024-12-04 17:44:55.160050
 
 """
 from typing import Sequence, Union
@@ -12,16 +12,49 @@
 
 
 # revision identifiers, used by Alembic.
-revision: str = '74f7f1590fb6'
-down_revision: Union[str, None] = '4a908d10b459'
+revision: str = '52101c205c9d'
+down_revision: Union[str, None] = None
 branch_labels: Union[str, Sequence[str], None] = None
 depends_on: Union[str, Sequence[str], None] = None
 
 
 def upgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('provenance',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('pipeline_name', sa.String(length=255), nullable=True),
+    sa.Column('version', sa.String(length=50), nullable=True),
+    sa.Column('compute', sa.Text(), nullable=True),
+    sa.Column('personnel', sa.Text(), nullable=True),
+    sa.Column('comment', sa.Text(), nullable=True),
+    sa.PrimaryKeyConstraint('id', name=op.f('pk_provenance'))
+    )
+    op.create_table('documents',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('hash_data', sa.String(), nullable=False),
+    sa.Column('created_at', sa.DateTime(), nullable=True),
+    sa.Column('s3uri', sa.Text(), nullable=False),
+    sa.Column('provenance_id', sa.Integer(), nullable=True),
+    sa.ForeignKeyConstraint(['provenance_id'], ['provenance.id'], name=op.f('fk_documents_provenance_id_provenance')),
+    sa.PrimaryKeyConstraint('id', name=op.f('pk_documents')),
+    sa.UniqueConstraint('hash_data', name=op.f('uq_documents_hash_data'))
+    )
+    op.create_table('works',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('created_at', sa.DateTime(), nullable=True),
+    sa.Column('modified_at', sa.DateTime(), nullable=True),
+    sa.Column('initial_document_id', sa.Integer(), nullable=True),
+    sa.Column('primary_document_id', sa.Integer(), nullable=True),
+    sa.Column('provenance_id', sa.Integer(), nullable=True),
+    sa.ForeignKeyConstraint(['initial_document_id'], ['documents.id'], name=op.f('fk_works_initial_document_id_documents')),
+    sa.ForeignKeyConstraint(['primary_document_id'], ['documents.id'], name=op.f('fk_works_primary_document_id_documents')),
+    sa.ForeignKeyConstraint(['provenance_id'], ['provenance.id'], name=op.f('fk_works_provenance_id_provenance')),
+    sa.PrimaryKeyConstraint('id', name=op.f('pk_works'))
+    )
     op.create_table('rtransparent_publication',
     sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('title', sa.String(), nullable=True),
+    sa.Column('author', sa.String(), nullable=True),
     sa.Column('is_open_code', sa.Boolean(), nullable=True),
     sa.Column('is_open_data', sa.Boolean(), nullable=True),
     sa.Column('year', sa.Integer(), nullable=True),
@@ -161,7 +194,6 @@ def upgrade() -> None:
     sa.Column('affiliation_aff_id', sa.String(), nullable=True),
     sa.Column('affiliation_all', sa.String(), nullable=True),
     sa.Column('article', sa.String(), nullable=True),
-    sa.Column('author', sa.String(), nullable=True),
     sa.Column('author_aff_id', sa.String(), nullable=True),
     sa.Column('correspondence', sa.String(), nullable=True),
     sa.Column('date_epub', sa.String(), nullable=True),
@@ -191,19 +223,22 @@ def upgrade() -> None:
     sa.Column('pmcid_uid', sa.String(), nullable=True),
     sa.Column('publisher_id', sa.String(), nullable=True),
     sa.Column('subject', sa.String(), nullable=True),
-    sa.Column('title', sa.String(), nullable=True),
     sa.Column('is_data_pred', sa.Boolean(), nullable=True),
     sa.Column('is_code_pred', sa.Boolean(), nullable=True),
-    sa.Column('work_id', sa.Integer(), nullable=False),
-    sa.Column('provenance_id', sa.Integer(), nullable=False),
-    sa.ForeignKeyConstraint(['provenance_id'], ['provenance.id'], ),
-    sa.ForeignKeyConstraint(['work_id'], ['works.id'], ),
-    sa.PrimaryKeyConstraint('id')
+    sa.Column('funder', sa.String(), nullable=True),
+    sa.Column('work_id', sa.Integer(), nullable=True),
+    sa.Column('provenance_id', sa.Integer(), nullable=True),
+    sa.ForeignKeyConstraint(['provenance_id'], ['provenance.id'], name=op.f('fk_rtransparent_publication_provenance_id_provenance')),
+    sa.ForeignKeyConstraint(['work_id'], ['works.id'], name=op.f('fk_rtransparent_publication_work_id_works')),
+    sa.PrimaryKeyConstraint('id', name=op.f('pk_rtransparent_publication'))
     )
     # ### end Alembic commands ###
 
 
 def downgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
     op.drop_table('rtransparent_publication')
+    op.drop_table('works')
+    op.drop_table('documents')
+    op.drop_table('provenance')
     # ### end Alembic commands ###