Working on #1 - FDA import process works. 3 hours for first import, 1.25 hours on subsequent updates.

2013-10-27 18:33:30 -04:00
parent e2bc602264
commit e0232aa02d
13 changed files with 575 additions and 71 deletions
--- a/alembic/versions/5ac93692b0ab_initial_revision.py
+++ b/alembic/versions/5ac93692b0ab_initial_revision.py
@@ -0,0 +1,125 @@
+"""Initial revision
+
+Revision ID: 5ac93692b0ab
+Revises: None
+Create Date: 2013-10-26 13:25:27.853595
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = '5ac93692b0ab'
+down_revision = None
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+def upgrade():
+    ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('drugbank_manufacturers',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('name', sa.String(), nullable=False),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_table('drugbank_packagers',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('name', sa.String(), nullable=False),
+    sa.Column('url', sa.String(), nullable=True),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_table('drugbank_categories',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('name', sa.String(), nullable=False),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_table('fda_products',
+    sa.Column('id', sa.String(), nullable=False),
+    sa.Column('ndc', sa.String(), nullable=False),
+    sa.Column('type', sa.String(), nullable=False),
+    sa.Column('proprietaryName', sa.String(), nullable=False),
+    sa.Column('proprietaryNameSuffix', sa.String(), nullable=True),
+    sa.Column('genericName', sa.String(), nullable=False),
+    sa.Column('marketingCategoryName', sa.String(), nullable=False),
+    sa.Column('labelerName', sa.String(), nullable=False),
+    sa.Column('deaSchedule', sa.String(), nullable=False),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_table('drugbank_drugs',
+    sa.Column('id', sa.String(), nullable=False),
+    sa.Column('name', sa.String(), nullable=False),
+    sa.Column('indication', sa.String(), nullable=False),
+    sa.Column('ndc_id', sa.String(), nullable=True),
+    sa.Column('wikipedia', sa.String(), nullable=True),
+    sa.ForeignKeyConstraint(['ndc_id'], ['fda_products.id'], ),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('id')
+    )
+    op.create_table('fda_product_substances',
+    sa.Column('fda_product_id', sa.String(), nullable=False),
+    sa.Column('substanceName', sa.String(), nullable=False),
+    sa.Column('strengthNumber', sa.Float(), nullable=False),
+    sa.Column('strengthUnit', sa.String(), nullable=False),
+    sa.Column('pharmaClasses', postgresql.ARRAY(sa.String()), nullable=False),
+    sa.ForeignKeyConstraint(['fda_product_id'], ['fda_products.id'], ),
+    sa.PrimaryKeyConstraint('fda_product_id')
+    )
+    op.create_table('drugbank_synonyms',
+    sa.Column('drug_id', sa.String(), nullable=False),
+    sa.Column('name', sa.String(), nullable=False),
+    sa.ForeignKeyConstraint(['drug_id'], ['drugbank_drugs.id'], ),
+    sa.PrimaryKeyConstraint('drug_id')
+    )
+    op.create_table('drugbank_packager_maps',
+    sa.Column('drug_id', sa.String(), nullable=False),
+    sa.Column('packager_id', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['drug_id'], ['drugbank_drugs.id'], ),
+    sa.ForeignKeyConstraint(['packager_id'], ['drugbank_packagers.id'], ),
+    sa.PrimaryKeyConstraint('drug_id')
+    )
+    op.create_table('drugbank_genericnames',
+    sa.Column('drug_id', sa.String(), nullable=False),
+    sa.Column('name', sa.String(), nullable=False),
+    sa.ForeignKeyConstraint(['drug_id'], ['drugbank_drugs.id'], ),
+    sa.PrimaryKeyConstraint('drug_id')
+    )
+    op.create_table('drugbank_prices',
+    sa.Column('drug_id', sa.String(), nullable=False),
+    sa.Column('description', sa.String(), nullable=False),
+    sa.Column('currency', sa.String(), nullable=False),
+    sa.Column('cost', sa.Float(), nullable=False),
+    sa.Column('unit', sa.String(), nullable=False),
+    sa.ForeignKeyConstraint(['drug_id'], ['drugbank_drugs.id'], ),
+    sa.PrimaryKeyConstraint('drug_id')
+    )
+    op.create_table('drugbank_manufacturer_maps',
+    sa.Column('drug_id', sa.String(), nullable=False),
+    sa.Column('manufacturer_id', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['drug_id'], ['drugbank_drugs.id'], ),
+    sa.ForeignKeyConstraint(['manufacturer_id'], ['drugbank_manufacturers.id'], ),
+    sa.PrimaryKeyConstraint('drug_id')
+    )
+    op.create_table('drugbank_category_maps',
+    sa.Column('drug_id', sa.String(), nullable=False),
+    sa.Column('category_id', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['category_id'], ['drugbank_categories.id'], ),
+    sa.ForeignKeyConstraint(['drug_id'], ['drugbank_drugs.id'], ),
+    sa.PrimaryKeyConstraint('drug_id')
+    )
+    ### end Alembic commands ###
+
+
+def downgrade():
+    ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('drugbank_category_maps')
+    op.drop_table('drugbank_manufacturer_maps')
+    op.drop_table('drugbank_prices')
+    op.drop_table('drugbank_genericnames')
+    op.drop_table('drugbank_packager_maps')
+    op.drop_table('drugbank_synonyms')
+    op.drop_table('fda_product_substances')
+    op.drop_table('drugbank_drugs')
+    op.drop_table('fda_products')
+    op.drop_table('drugbank_categories')
+    op.drop_table('drugbank_packagers')
+    op.drop_table('drugbank_manufacturers')
+    ### end Alembic commands ###