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Database updates, scraping samples from excel sheets

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This commit is contained in:
Landon Wark
2023-01-19 11:22:57 -06:00
parent e763e7273d
commit d17ee5862d
10 changed files with 206 additions and 53 deletions
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60
alembic/versions/4cba0c1ffe03_initial_commit.py → alembic/versions/03da9270e51f_initial_commit.py
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@@ -1,8 +1,8 @@
"""initial commit
Revision ID: 4cba0c1ffe03
Revision ID: 03da9270e51f
Revises:
Create Date: 2023-01-18 08:59:34.382715
Create Date: 2023-01-19 09:01:03.022482
"""
from alembic import op
@@ -10,7 +10,7 @@ import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '4cba0c1ffe03'
revision = '03da9270e51f'
down_revision = None
branch_labels = None
depends_on = None
@@ -50,22 +50,6 @@ def upgrade() -> None:
sa.ForeignKeyConstraint(['kit_id'], ['_kits.id'], name='fk_RT_kits_id', ondelete='SET NULL', use_alter=True),
sa.PrimaryKeyConstraint('id')
)
op.create_table('_ww_samples',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('ww_processing_num', sa.String(length=64), nullable=True),
sa.Column('ww_sample_full_id', sa.String(length=64), nullable=True),
sa.Column('rsl_number', sa.String(length=64), nullable=True),
sa.Column('collection_date', sa.TIMESTAMP(), nullable=True),
sa.Column('testing_type', sa.String(length=64), nullable=True),
sa.Column('site_status', sa.String(length=64), nullable=True),
sa.Column('notes', sa.String(length=2000), nullable=True),
sa.Column('ct_n1', sa.FLOAT(precision=2), nullable=True),
sa.Column('ct_n2', sa.FLOAT(precision=2), nullable=True),
sa.Column('seq_submitted', sa.BOOLEAN(), nullable=True),
sa.Column('ww_seq_run_id', sa.String(length=64), nullable=True),
sa.Column('sample_type', sa.String(length=8), nullable=True),
sa.PrimaryKeyConstraint('id')
)
op.create_table('_control_samples',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('parent_id', sa.String(), nullable=True),
@@ -119,35 +103,63 @@ def upgrade() -> None:
sa.Column('technician', sa.String(length=64), nullable=True),
sa.Column('reagents_id', sa.String(), nullable=True),
sa.Column('control_id', sa.INTEGER(), nullable=True),
sa.Column('sample_id', sa.String(), nullable=True),
sa.ForeignKeyConstraint(['control_id'], ['_control_samples.id'], name='fk_BC_control_id', ondelete='SET NULL'),
sa.ForeignKeyConstraint(['extraction_kit_id'], ['_kits.id'], ondelete='SET NULL'),
sa.ForeignKeyConstraint(['extraction_kit_id'], ['_kits.id'], name='fk_BS_extkit_id', ondelete='SET NULL'),
sa.ForeignKeyConstraint(['reagents_id'], ['_reagents.id'], name='fk_BS_reagents_id', ondelete='SET NULL'),
sa.ForeignKeyConstraint(['sample_id'], ['_ww_samples.id'], name='fk_WW_sample_id', ondelete='SET NULL'),
sa.ForeignKeyConstraint(['submitting_lab_id'], ['_organizations.id'], ondelete='SET NULL'),
sa.ForeignKeyConstraint(['submitting_lab_id'], ['_organizations.id'], name='fk_BS_sublab_id', ondelete='SET NULL'),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('rsl_plate_num'),
sa.UniqueConstraint('submitter_plate_num')
)
op.create_table('_bc_samples',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('well_number', sa.String(length=8), nullable=True),
sa.Column('sample_id', sa.String(length=64), nullable=False),
sa.Column('organism', sa.String(length=64), nullable=True),
sa.Column('concentration', sa.String(length=16), nullable=True),
sa.Column('rsl_plate_id', sa.INTEGER(), nullable=True),
sa.ForeignKeyConstraint(['rsl_plate_id'], ['_submissions.id'], name='fk_BCS_sample_id', ondelete='SET NULL'),
sa.PrimaryKeyConstraint('id')
)
op.create_table('_reagents_submissions',
sa.Column('reagent_id', sa.INTEGER(), nullable=True),
sa.Column('submission_id', sa.INTEGER(), nullable=True),
sa.ForeignKeyConstraint(['reagent_id'], ['_reagents.id'], ),
sa.ForeignKeyConstraint(['submission_id'], ['_submissions.id'], )
)
op.create_table('_ww_samples',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('ww_processing_num', sa.String(length=64), nullable=True),
sa.Column('ww_sample_full_id', sa.String(length=64), nullable=False),
sa.Column('rsl_number', sa.String(length=64), nullable=True),
sa.Column('rsl_plate_id', sa.INTEGER(), nullable=True),
sa.Column('collection_date', sa.TIMESTAMP(), nullable=True),
sa.Column('testing_type', sa.String(length=64), nullable=True),
sa.Column('site_status', sa.String(length=64), nullable=True),
sa.Column('notes', sa.String(length=2000), nullable=True),
sa.Column('ct_n1', sa.FLOAT(precision=2), nullable=True),
sa.Column('ct_n2', sa.FLOAT(precision=2), nullable=True),
sa.Column('seq_submitted', sa.BOOLEAN(), nullable=True),
sa.Column('ww_seq_run_id', sa.String(length=64), nullable=True),
sa.Column('sample_type', sa.String(length=8), nullable=True),
sa.Column('well_number', sa.String(length=8), nullable=True),
sa.ForeignKeyConstraint(['rsl_plate_id'], ['_submissions.id'], name='fk_WWS_sample_id', ondelete='SET NULL'),
sa.PrimaryKeyConstraint('id')
)
# ### end Alembic commands ###
def downgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
op.drop_table('_ww_samples')
op.drop_table('_reagents_submissions')
op.drop_table('_bc_samples')
op.drop_table('_submissions')
op.drop_table('_orgs_contacts')
op.drop_table('_reagentstypes_kittypes')
op.drop_table('_reagents')
op.drop_table('_organizations')
op.drop_table('_control_samples')
op.drop_table('_ww_samples')
op.drop_table('_reagent_types')
op.drop_table('_kits')
op.drop_table('_control_types')