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Big update, semi-functional

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This commit is contained in:
Landon Wark
2023-08-28 13:20:30 -05:00
parent b6de159631
commit bc7a3b8f5f
13 changed files with 824 additions and 466 deletions
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52
alembic/versions/b879020f2a91_rebuild_database.py → alembic/versions/cac89ced412b_rebuild_database.py
View File

@@ -1,8 +1,8 @@
"""rebuild database
Revision ID: b879020f2a91
Revision ID: cac89ced412b
Revises:
Create Date: 2023-08-02 09:16:12.792995
Create Date: 2023-08-25 14:03:48.883090
"""
from alembic import op
@@ -10,7 +10,7 @@ import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = 'b879020f2a91'
revision = 'cac89ced412b'
down_revision = None
branch_labels = None
depends_on = None
@@ -35,11 +35,6 @@ def upgrade() -> None:
op.create_table('_kits',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('name', sa.String(length=64), nullable=True),
sa.Column('used_for', sa.JSON(), nullable=True),
sa.Column('cost_per_run', sa.FLOAT(precision=2), nullable=True),
sa.Column('mutable_cost_column', sa.FLOAT(precision=2), nullable=True),
sa.Column('mutable_cost_sample', sa.FLOAT(precision=2), nullable=True),
sa.Column('constant_cost', sa.FLOAT(precision=2), nullable=True),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('name')
)
@@ -61,24 +56,24 @@ def upgrade() -> None:
sa.Column('submitter_id', sa.String(length=64), nullable=False),
sa.Column('sample_type', sa.String(length=32), nullable=True),
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('received_date', sa.TIMESTAMP(), 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('n1_status', sa.String(length=32), nullable=True),
sa.Column('n2_status', sa.String(length=32), nullable=True),
sa.Column('seq_submitted', sa.BOOLEAN(), nullable=True),
sa.Column('ww_seq_run_id', sa.String(length=64), nullable=True),
sa.Column('pcr_results', sa.JSON(), nullable=True),
sa.Column('well_24', sa.String(length=8), nullable=True),
sa.Column('sample_location', sa.String(length=8), nullable=True),
sa.Column('organism', sa.String(length=64), nullable=True),
sa.Column('concentration', sa.String(length=16), nullable=True),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('submitter_id')
)
op.create_table('_submission_types',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('name', sa.String(length=128), nullable=True),
sa.Column('info_map', sa.JSON(), nullable=True),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('name')
)
op.create_table('_discounts',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('kit_id', sa.INTEGER(), nullable=True),
@@ -113,6 +108,16 @@ def upgrade() -> None:
sa.ForeignKeyConstraint(['reagent_types_id'], ['_reagent_types.id'], ),
sa.PrimaryKeyConstraint('reagent_types_id', 'kits_id')
)
op.create_table('_submissiontypes_kittypes',
sa.Column('submission_types_id', sa.INTEGER(), nullable=False),
sa.Column('kits_id', sa.INTEGER(), nullable=False),
sa.Column('mutable_cost_column', sa.FLOAT(precision=2), nullable=True),
sa.Column('mutable_cost_sample', sa.FLOAT(precision=2), nullable=True),
sa.Column('constant_cost', sa.FLOAT(precision=2), nullable=True),
sa.ForeignKeyConstraint(['kits_id'], ['_kits.id'], ),
sa.ForeignKeyConstraint(['submission_types_id'], ['_submission_types.id'], ),
sa.PrimaryKeyConstraint('submission_types_id', 'kits_id')
)
op.create_table('_submissions',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('rsl_plate_num', sa.String(length=32), nullable=False),
@@ -121,7 +126,7 @@ def upgrade() -> None:
sa.Column('submitting_lab_id', sa.INTEGER(), nullable=True),
sa.Column('sample_count', sa.INTEGER(), nullable=True),
sa.Column('extraction_kit_id', sa.INTEGER(), nullable=True),
sa.Column('submission_type', sa.String(length=32), nullable=True),
sa.Column('submission_type_name', sa.String(), nullable=True),
sa.Column('technician', sa.String(length=64), nullable=True),
sa.Column('reagents_id', sa.String(), nullable=True),
sa.Column('extraction_info', sa.JSON(), nullable=True),
@@ -131,6 +136,7 @@ def upgrade() -> None:
sa.Column('pcr_info', sa.JSON(), nullable=True),
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(['submission_type_name'], ['_submission_types.name'], name='fk_BS_subtype_name', 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'),
@@ -164,6 +170,12 @@ def upgrade() -> None:
sa.Column('submission_id', sa.INTEGER(), nullable=False),
sa.Column('row', sa.INTEGER(), nullable=True),
sa.Column('column', sa.INTEGER(), nullable=True),
sa.Column('base_sub_type', sa.String(), nullable=True),
sa.Column('ct_n1', sa.FLOAT(precision=2), nullable=True),
sa.Column('ct_n2', sa.FLOAT(precision=2), nullable=True),
sa.Column('n1_status', sa.String(length=32), nullable=True),
sa.Column('n2_status', sa.String(length=32), nullable=True),
sa.Column('pcr_results', sa.JSON(), nullable=True),
sa.ForeignKeyConstraint(['sample_id'], ['_samples.id'], ),
sa.ForeignKeyConstraint(['submission_id'], ['_submissions.id'], ),
sa.PrimaryKeyConstraint('sample_id', 'submission_id')
@@ -177,10 +189,12 @@ def downgrade() -> None:
op.drop_table('_reagents_submissions')
op.drop_table('_control_samples')
op.drop_table('_submissions')
op.drop_table('_submissiontypes_kittypes')
op.drop_table('_reagenttypes_kittypes')
op.drop_table('_reagents')
op.drop_table('_orgs_contacts')
op.drop_table('_discounts')
op.drop_table('_submission_types')
op.drop_table('_samples')
op.drop_table('_reagent_types')
op.drop_table('_organizations')

56
alembic/versions/da94eca9d381_polymorpherizing_associations.py
View File

@@ -1,56 +0,0 @@
"""polymorpherizing associations
Revision ID: da94eca9d381
Revises: b879020f2a91
Create Date: 2023-08-03 13:30:34.056316
"""
from alembic import op
import sqlalchemy as sa
from sqlalchemy.dialects import sqlite
# revision identifiers, used by Alembic.
revision = 'da94eca9d381'
down_revision = 'b879020f2a91'
branch_labels = None
depends_on = None
def upgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('_samples', schema=None) as batch_op:
batch_op.drop_column('ct_n2')
batch_op.drop_column('n1_status')
batch_op.drop_column('pcr_results')
batch_op.drop_column('n2_status')
batch_op.drop_column('ct_n1')
with op.batch_alter_table('_submission_sample', schema=None) as batch_op:
batch_op.add_column(sa.Column('base_sub_type', sa.String(), nullable=True))
batch_op.add_column(sa.Column('ct_n1', sa.FLOAT(precision=2), nullable=True))
batch_op.add_column(sa.Column('ct_n2', sa.FLOAT(precision=2), nullable=True))
batch_op.add_column(sa.Column('n1_status', sa.String(length=32), nullable=True))
batch_op.add_column(sa.Column('n2_status', sa.String(length=32), nullable=True))
batch_op.add_column(sa.Column('pcr_results', sa.JSON(), nullable=True))
# ### end Alembic commands ###
def downgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('_submission_sample', schema=None) as batch_op:
batch_op.drop_column('pcr_results')
batch_op.drop_column('n2_status')
batch_op.drop_column('n1_status')
batch_op.drop_column('ct_n2')
batch_op.drop_column('ct_n1')
batch_op.drop_column('base_sub_type')
with op.batch_alter_table('_samples', schema=None) as batch_op:
batch_op.add_column(sa.Column('ct_n1', sa.FLOAT(), nullable=True))
batch_op.add_column(sa.Column('n2_status', sa.VARCHAR(length=32), nullable=True))
batch_op.add_column(sa.Column('pcr_results', sqlite.JSON(), nullable=True))
batch_op.add_column(sa.Column('n1_status', sa.VARCHAR(length=32), nullable=True))
batch_op.add_column(sa.Column('ct_n2', sa.FLOAT(), nullable=True))
# ### end Alembic commands ###