Prior to major database rebuild.

2023-07-27 08:14:04 -05:00
parent f22e697815
commit af810ae528
22 changed files with 76 additions and 696 deletions
--- a/alembic/versions/00de69ad6eab_added_target_status_to_ww_samples.py
+++ b/alembic/versions/00de69ad6eab_added_target_status_to_ww_samples.py
@@ -1,57 +0,0 @@
-"""added target status to ww samples
-
-Revision ID: 00de69ad6eab
-Revises: 8adc85dd9b92
-Create Date: 2023-03-31 14:51:40.705301
-
-"""
-from alembic import op
-import sqlalchemy as sa
-from sqlalchemy.dialects import sqlite
-
-# revision identifiers, used by Alembic.
-revision = '00de69ad6eab'
-down_revision = '8adc85dd9b92'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    # op.drop_table('_alembic_tmp__submissions')
-    with op.batch_alter_table('_ww_samples', schema=None) as batch_op:
-        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))
-
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_ww_samples', schema=None) as batch_op:
-        batch_op.drop_column('n2_status')
-        batch_op.drop_column('n1_status')
-
-    # op.create_table('_alembic_tmp__submissions',
-    # sa.Column('id', sa.INTEGER(), nullable=False),
-    # sa.Column('rsl_plate_num', sa.VARCHAR(length=32), nullable=False),
-    # sa.Column('submitter_plate_num', sa.VARCHAR(length=127), nullable=True),
-    # sa.Column('submitted_date', sa.TIMESTAMP(), nullable=True),
-    # 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.VARCHAR(length=32), nullable=True),
-    # sa.Column('technician', sa.VARCHAR(length=64), nullable=True),
-    # sa.Column('reagents_id', sa.VARCHAR(), nullable=True),
-    # sa.Column('extraction_info', sqlite.JSON(), nullable=True),
-    # sa.Column('run_cost', sa.FLOAT(), nullable=True),
-    # sa.Column('uploaded_by', sa.VARCHAR(length=32), nullable=True),
-    # sa.Column('pcr_info', sqlite.JSON(), nullable=True),
-    # sa.ForeignKeyConstraint(['extraction_kit_id'], ['_kits.id'], ondelete='SET NULL'),
-    # sa.ForeignKeyConstraint(['reagents_id'], ['_reagents.id'], ondelete='SET NULL'),
-    # sa.ForeignKeyConstraint(['submitting_lab_id'], ['_organizations.id'], ondelete='SET NULL'),
-    # sa.PrimaryKeyConstraint('id'),
-    # sa.UniqueConstraint('rsl_plate_num'),
-    # sa.UniqueConstraint('submitter_plate_num')
-    # )
-    # ### end Alembic commands ###
--- a/alembic/versions/06e2c8dc4889_database_rebuild.py
+++ b/alembic/versions/06e2c8dc4889_database_rebuild.py
@@ -1,8 +1,8 @@
-"""initial commit
+"""database_rebuild

-Revision ID: 8753ed70f148
+Revision ID: 06e2c8dc4889
 Revises: 
-Create Date: 2023-01-26 12:48:42.340619
+Create Date: 2023-07-26 14:08:18.809998

 """
 from alembic import op
@@ -10,7 +10,7 @@ import sqlalchemy as sa


 # revision identifiers, used by Alembic.
-revision = '8753ed70f148'
+revision = '06e2c8dc4889'
 down_revision = None
 branch_labels = None
 depends_on = None
@@ -23,6 +23,8 @@ def upgrade() -> None:
    sa.Column('name', sa.String(length=64), nullable=True),
    sa.Column('email', sa.String(length=64), nullable=True),
    sa.Column('phone', sa.String(length=32), nullable=True),
+    sa.Column('organization_id', sa.INTEGER(), nullable=True),
+    sa.ForeignKeyConstraint(['organization_id'], ['_organizations.id'], name='fk_contact_org_id', ondelete='SET NULL'),
    sa.PrimaryKeyConstraint('id')
    )
    op.create_table('_control_types',
@@ -37,19 +39,14 @@ def upgrade() -> None:
    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.Column('reagent_types_id', sa.INTEGER(), nullable=True),
    sa.ForeignKeyConstraint(['reagent_types_id'], ['_reagent_types.id'], name='fk_KT_reagentstype_id', ondelete='SET NULL', use_alter=True),
    sa.PrimaryKeyConstraint('id'),
    sa.UniqueConstraint('name')
    )
-    op.create_table('_reagent_types',
-    sa.Column('id', sa.INTEGER(), nullable=False),
-    sa.Column('name', sa.String(length=64), nullable=True),
-    sa.Column('kit_id', sa.INTEGER(), nullable=True),
-    sa.Column('eol_ext', sa.Interval(), nullable=True),
-    sa.ForeignKeyConstraint(['kit_id'], ['_kits.id'], name='fk_RT_kits_id', ondelete='SET NULL', use_alter=True),
-    sa.PrimaryKeyConstraint('id')
-    )
    op.create_table('_organizations',
    sa.Column('id', sa.INTEGER(), nullable=False),
    sa.Column('name', sa.String(length=64), nullable=True),
@@ -58,6 +55,32 @@ def upgrade() -> None:
    sa.ForeignKeyConstraint(['contact_ids'], ['_contacts.id'], name='fk_org_contact_id', ondelete='SET NULL'),
    sa.PrimaryKeyConstraint('id')
    )
+    op.create_table('_reagent_types',
+    sa.Column('id', sa.INTEGER(), nullable=False),
+    sa.Column('name', sa.String(length=64), nullable=True),
+    sa.Column('kit_id', sa.INTEGER(), nullable=True),
+    sa.Column('eol_ext', sa.Interval(), nullable=True),
+    sa.Column('required', sa.INTEGER(), server_default='1', nullable=True),
+    sa.Column('last_used', sa.String(length=32), nullable=True),
+    sa.ForeignKeyConstraint(['kit_id'], ['_kits.id'], name='fk_RT_kits_id', ondelete='SET NULL', use_alter=True),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_table('_discounts',
+    sa.Column('id', sa.INTEGER(), nullable=False),
+    sa.Column('kit_id', sa.INTEGER(), nullable=True),
+    sa.Column('client_id', sa.INTEGER(), nullable=True),
+    sa.Column('name', sa.String(length=128), nullable=True),
+    sa.Column('amount', sa.FLOAT(precision=2), nullable=True),
+    sa.ForeignKeyConstraint(['client_id'], ['_organizations.id'], name='fk_org_id', ondelete='SET NULL'),
+    sa.ForeignKeyConstraint(['kit_id'], ['_kits.id'], name='fk_kit_type_id', ondelete='SET NULL'),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_table('_orgs_contacts',
+    sa.Column('org_id', sa.INTEGER(), nullable=True),
+    sa.Column('contact_id', sa.INTEGER(), nullable=True),
+    sa.ForeignKeyConstraint(['contact_id'], ['_contacts.id'], ),
+    sa.ForeignKeyConstraint(['org_id'], ['_organizations.id'], )
+    )
    op.create_table('_reagents',
    sa.Column('id', sa.INTEGER(), nullable=False),
    sa.Column('type_id', sa.INTEGER(), nullable=True),
@@ -73,15 +96,9 @@ def upgrade() -> None:
    sa.ForeignKeyConstraint(['kits_id'], ['_kits.id'], ),
    sa.ForeignKeyConstraint(['reagent_types_id'], ['_reagent_types.id'], )
    )
-    op.create_table('_orgs_contacts',
-    sa.Column('org_id', sa.INTEGER(), nullable=True),
-    sa.Column('contact_id', sa.INTEGER(), nullable=True),
-    sa.ForeignKeyConstraint(['contact_id'], ['_contacts.id'], ),
-    sa.ForeignKeyConstraint(['org_id'], ['_organizations.id'], )
-    )
    op.create_table('_submissions',
    sa.Column('id', sa.INTEGER(), nullable=False),
-    sa.Column('rsl_plate_num', sa.String(length=32), nullable=True),
+    sa.Column('rsl_plate_num', sa.String(length=32), nullable=False),
    sa.Column('submitter_plate_num', sa.String(length=127), nullable=True),
    sa.Column('submitted_date', sa.TIMESTAMP(), nullable=True),
    sa.Column('submitting_lab_id', sa.INTEGER(), nullable=True),
@@ -90,6 +107,11 @@ def upgrade() -> None:
    sa.Column('submission_type', sa.String(length=32), 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),
+    sa.Column('run_cost', sa.FLOAT(precision=2), nullable=True),
+    sa.Column('uploaded_by', sa.String(length=32), nullable=True),
+    sa.Column('comment', sa.JSON(), nullable=True),
+    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(['submitting_lab_id'], ['_organizations.id'], name='fk_BS_sublab_id', ondelete='SET NULL'),
@@ -105,7 +127,8 @@ def upgrade() -> None:
    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')
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('sample_id')
    )
    op.create_table('_control_samples',
    sa.Column('id', sa.INTEGER(), nullable=False),
@@ -116,6 +139,9 @@ def upgrade() -> None:
    sa.Column('matches', sa.JSON(), nullable=True),
    sa.Column('kraken', sa.JSON(), nullable=True),
    sa.Column('submission_id', sa.INTEGER(), nullable=True),
+    sa.Column('refseq_version', sa.String(length=16), nullable=True),
+    sa.Column('kraken2_version', sa.String(length=16), nullable=True),
+    sa.Column('kraken2_db_version', sa.String(length=32), nullable=True),
    sa.ForeignKeyConstraint(['parent_id'], ['_control_types.id'], name='fk_control_parent_id'),
    sa.ForeignKeyConstraint(['submission_id'], ['_submissions.id'], ),
    sa.PrimaryKeyConstraint('id'),
@@ -134,17 +160,23 @@ def upgrade() -> None:
    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('well_number', sa.String(length=8), 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('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('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')
+    sa.Column('pcr_results', sa.JSON(), nullable=True),
+    sa.Column('well_24', sa.String(length=8), nullable=True),
+    sa.Column('artic_well_number', sa.String(length=8), nullable=True),
+    sa.ForeignKeyConstraint(['rsl_plate_id'], ['_submissions.id'], name='fk_WWS_submission_id', ondelete='SET NULL'),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('ww_sample_full_id')
    )
    # ### end Alembic commands ###

@@ -156,11 +188,12 @@ def downgrade() -> None:
    op.drop_table('_control_samples')
    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('_orgs_contacts')
+    op.drop_table('_discounts')
    op.drop_table('_reagent_types')
+    op.drop_table('_organizations')
    op.drop_table('_kits')
    op.drop_table('_control_types')
    op.drop_table('_contacts')
--- a/alembic/versions/0ee7ffa026b2_added_pcr_info_to_wastewater_subs.py
+++ b/alembic/versions/0ee7ffa026b2_added_pcr_info_to_wastewater_subs.py
@@ -1,32 +0,0 @@
-"""added pcr info to wastewater subs
-
-Revision ID: 0ee7ffa026b2
-Revises: 3d80e4a17a26
-Create Date: 2023-03-22 14:51:37.871062
-
-"""
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = '0ee7ffa026b2'
-down_revision = '3d80e4a17a26'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_submissions', schema=None) as batch_op:
-        batch_op.add_column(sa.Column('pcr_info', sa.JSON(), nullable=True))
-        
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_submissions', schema=None) as batch_op:
-        batch_op.drop_column('pcr_info')
-
-    # ### end Alembic commands ###
--- a/alembic/versions/178203610c3b_updating_costs.py
+++ b/alembic/versions/178203610c3b_updating_costs.py
@@ -1,40 +0,0 @@
-"""updating costs
-
-Revision ID: 178203610c3b
-Revises: afbdd9e46207
-Create Date: 2023-02-02 09:31:05.748477
-
-"""
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = '178203610c3b'
-down_revision = 'afbdd9e46207'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_kits', schema=None) as batch_op:
-        batch_op.add_column(sa.Column('mutable_cost', sa.FLOAT(precision=2), nullable=True))
-        batch_op.add_column(sa.Column('constant_cost', sa.FLOAT(precision=2), nullable=True))
-
-    with op.batch_alter_table('_submissions', schema=None) as batch_op:
-        batch_op.add_column(sa.Column('run_cost', sa.FLOAT(precision=2), nullable=True))
-
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_submissions', schema=None) as batch_op:
-        batch_op.drop_column('run_cost')
-
-    with op.batch_alter_table('_kits', schema=None) as batch_op:
-        batch_op.drop_column('constant_cost')
-        batch_op.drop_column('mutable_cost')
-
-    # ### end Alembic commands ###
--- a/alembic/versions/3d80e4a17a26_added_versions_to_ref_kraken.py
+++ b/alembic/versions/3d80e4a17a26_added_versions_to_ref_kraken.py
@@ -1,59 +0,0 @@
-"""added versions to ref/kraken
-
-Revision ID: 3d80e4a17a26
-Revises: 785bb1140878
-Create Date: 2023-03-02 13:09:30.750398
-
-"""
-from alembic import op
-import sqlalchemy as sa
-from sqlalchemy.dialects import sqlite
-
-# revision identifiers, used by Alembic.
-revision = '3d80e4a17a26'
-down_revision = '785bb1140878'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    # op.drop_table('_alembic_tmp__submissions')
-    with op.batch_alter_table('_control_samples', schema=None) as batch_op:
-        batch_op.add_column(sa.Column('refseq_version', sa.String(length=16), nullable=True))
-        batch_op.add_column(sa.Column('kraken2_version', sa.String(length=16), nullable=True))
-        batch_op.add_column(sa.Column('kraken2_db_version', sa.String(length=32), nullable=True))
-
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    
-    with op.batch_alter_table('_control_samples', schema=None) as batch_op:
-        batch_op.drop_column('kraken2_db_version')
-        batch_op.drop_column('kraken2_version')
-        batch_op.drop_column('refseq_version')
-
-    # op.create_table('_alembic_tmp__submissions',
-    # sa.Column('id', sa.INTEGER(), nullable=False),
-    # sa.Column('rsl_plate_num', sa.VARCHAR(length=32), nullable=False),
-    # sa.Column('submitter_plate_num', sa.VARCHAR(length=127), nullable=True),
-    # sa.Column('submitted_date', sa.TIMESTAMP(), nullable=True),
-    # 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.VARCHAR(length=32), nullable=True),
-    # sa.Column('technician', sa.VARCHAR(length=64), nullable=True),
-    # sa.Column('reagents_id', sa.VARCHAR(), nullable=True),
-    # sa.Column('extraction_info', sqlite.JSON(), nullable=True),
-    # sa.Column('run_cost', sa.FLOAT(), nullable=True),
-    # sa.Column('uploaded_by', sa.VARCHAR(length=32), nullable=True),
-    # sa.ForeignKeyConstraint(['extraction_kit_id'], ['_kits.id'], ondelete='SET NULL'),
-    # sa.ForeignKeyConstraint(['reagents_id'], ['_reagents.id'], ondelete='SET NULL'),
-    # sa.ForeignKeyConstraint(['submitting_lab_id'], ['_organizations.id'], ondelete='SET NULL'),
-    # sa.PrimaryKeyConstraint('id'),
-    # sa.UniqueConstraint('rsl_plate_num'),
-    # sa.UniqueConstraint('submitter_plate_num')
-    # )
-    # ### end Alembic commands ###
--- a/alembic/versions/4c6221f01324_added_last_used_to_reagenttype.py
+++ b/alembic/versions/4c6221f01324_added_last_used_to_reagenttype.py
@@ -1,32 +0,0 @@
-"""added last_used to reagenttype
-
-Revision ID: 4c6221f01324
-Revises: 7aadd731ff63
-Create Date: 2023-07-07 14:32:24.064042
-
-"""
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = '4c6221f01324'
-down_revision = '7aadd731ff63'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_reagent_types', schema=None) as batch_op:
-        batch_op.add_column(sa.Column('last_used', sa.String(length=32), nullable=True))
-
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_reagent_types', schema=None) as batch_op:
-        batch_op.drop_column('last_used')
-
-    # ### end Alembic commands ###
--- a/alembic/versions/64fec6271a50_added_elution_well_to_ww_sample.py
+++ b/alembic/versions/64fec6271a50_added_elution_well_to_ww_sample.py
@@ -1,31 +0,0 @@
-"""added elution well to ww_sample
-
-Revision ID: 64fec6271a50
-Revises: a31943b2284c
-Create Date: 2023-05-24 14:43:25.477637
-
-"""
-from alembic import op
-import sqlalchemy as sa
-from sqlalchemy.dialects import sqlite
-
-# revision identifiers, used by Alembic.
-revision = '64fec6271a50'
-down_revision = 'a31943b2284c'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_ww_samples', schema=None) as batch_op:
-        batch_op.add_column(sa.Column('elution_well', sa.String(length=8), nullable=True))
-
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_ww_samples', schema=None) as batch_op:
-        batch_op.drop_column('elution_well')
-    # ### end Alembic commands ###
--- a/alembic/versions/78178df0286a_making_sample_ids_unique.py
+++ b/alembic/versions/78178df0286a_making_sample_ids_unique.py
@@ -1,38 +0,0 @@
-"""making sample ids unique
-
-Revision ID: 78178df0286a
-Revises: 4c6221f01324
-Create Date: 2023-07-26 13:55:41.864399
-
-"""
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = '78178df0286a'
-down_revision = '4c6221f01324'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_bc_samples', schema=None) as batch_op:
-        batch_op.create_unique_constraint("unique_bc_sample", ['sample_id'])
-
-    with op.batch_alter_table('_ww_samples', schema=None) as batch_op:
-        batch_op.create_unique_constraint("unique_ww_sample", ['ww_sample_full_id'])
-
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_ww_samples', schema=None) as batch_op:
-        batch_op.drop_constraint(None, type_='unique')
-
-    with op.batch_alter_table('_bc_samples', schema=None) as batch_op:
-        batch_op.drop_constraint(None, type_='unique')
-
-    # ### end Alembic commands ###
--- a/alembic/versions/785bb1140878_added_user_tracking.py
+++ b/alembic/versions/785bb1140878_added_user_tracking.py
@@ -1,32 +0,0 @@
-"""added user tracking
-
-Revision ID: 785bb1140878
-Revises: 178203610c3b
-Create Date: 2023-02-06 09:54:20.371117
-
-"""
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = '785bb1140878'
-down_revision = '178203610c3b'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_submissions', schema=None) as batch_op:
-        batch_op.add_column(sa.Column('uploaded_by', sa.String(length=32), nullable=True))
-
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_submissions', schema=None) as batch_op:
-        batch_op.drop_column('uploaded_by')
-
-    # ### end Alembic commands ###
--- a/alembic/versions/7aadd731ff63_added_required_to_reagenttype.py
+++ b/alembic/versions/7aadd731ff63_added_required_to_reagenttype.py
@@ -1,42 +0,0 @@
-"""added required to reagenttype
-
-Revision ID: 7aadd731ff63
-Revises: 8d32abdafe2b
-Create Date: 2023-07-06 07:58:36.545604
-
-"""
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = '7aadd731ff63'
-down_revision = '8d32abdafe2b'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_reagent_types', schema=None) as batch_op:
-        batch_op.add_column(sa.Column('required', sa.INTEGER(), nullable=True))
-
-    # with op.batch_alter_table('_submissions', schema=None) as batch_op:
-    #     batch_op.alter_column('rsl_plate_num',
-    #            existing_type=sa.VARCHAR(length=32),
-    #            nullable=False)
-
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    # with op.batch_alter_table('_submissions', schema=None) as batch_op:
-    #     batch_op.alter_column('rsl_plate_num',
-    #            existing_type=sa.VARCHAR(length=32),
-    #            nullable=True)
-
-    with op.batch_alter_table('_reagent_types', schema=None) as batch_op:
-        batch_op.drop_column('required')
-
-    # ### end Alembic commands ###
--- a/alembic/versions/83b06f3f4869_updated_discount_table.py
+++ b/alembic/versions/83b06f3f4869_updated_discount_table.py
@@ -1,30 +0,0 @@
-"""updated discount table
-
-Revision ID: 83b06f3f4869
-Revises: cc9672a505f5
-Create Date: 2023-04-27 13:04:35.886294
-
-"""
-from alembic import op
-import sqlalchemy as sa
-from sqlalchemy.dialects import sqlite
-
-# revision identifiers, used by Alembic.
-revision = '83b06f3f4869'
-down_revision = 'cc9672a505f5'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_discounts', schema=None) as batch_op:
-        batch_op.add_column(sa.Column('name', sa.String(length=128), nullable=True))
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_discounts', schema=None) as batch_op:
-        batch_op.drop_column('name')
-    # ### end Alembic commands ###
--- a/alembic/versions/8adc85dd9b92_added_pcr_info_to_wastewater_samples.py
+++ b/alembic/versions/8adc85dd9b92_added_pcr_info_to_wastewater_samples.py
@@ -1,31 +0,0 @@
-"""added pcr info to wastewater samples
-
-Revision ID: 8adc85dd9b92
-Revises: 0ee7ffa026b2
-Create Date: 2023-03-27 13:46:06.173379
-
-"""
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = '8adc85dd9b92'
-down_revision = '0ee7ffa026b2'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_ww_samples', schema=None) as batch_op:
-        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('_ww_samples', schema=None) as batch_op:
-        batch_op.drop_column('pcr_results')
-    # ### end Alembic commands ###
--- a/alembic/versions/8d32abdafe2b_moved_artic_info_to_ww_samples.py
+++ b/alembic/versions/8d32abdafe2b_moved_artic_info_to_ww_samples.py
@@ -1,30 +0,0 @@
-"""moved artic info to ww_samples
-
-Revision ID: 8d32abdafe2b
-Revises: aac569c672de
-Create Date: 2023-06-05 10:10:37.650733
-
-"""
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = '8d32abdafe2b'
-down_revision = 'aac569c672de'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_ww_samples', schema=None) as batch_op:
-        batch_op.add_column(sa.Column('artic_well_number', sa.String(length=8), nullable=True))
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_ww_samples', schema=None) as batch_op:
-        batch_op.drop_column('artic_well_number')
-    # ### end Alembic commands ###
--- a/alembic/versions/a31943b2284c_added_commenting.py
+++ b/alembic/versions/a31943b2284c_added_commenting.py
@@ -1,33 +0,0 @@
-"""added commenting
-
-Revision ID: a31943b2284c
-Revises: 83b06f3f4869
-Create Date: 2023-05-10 11:34:30.339915
-
-"""
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = 'a31943b2284c'
-down_revision = '83b06f3f4869'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_submissions', schema=None) as batch_op:
-        batch_op.add_column(sa.Column('comment', sa.JSON(), nullable=True))
-        
-
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_submissions', schema=None) as batch_op:
-        batch_op.drop_column('comment')
-
-    # ### end Alembic commands ###
--- a/alembic/versions/aac569c672de_added_in_artic_information.py
+++ b/alembic/versions/aac569c672de_added_in_artic_information.py
@@ -1,63 +0,0 @@
-"""added in artic information
-
-Revision ID: aac569c672de
-Revises: 64fec6271a50
-Create Date: 2023-06-02 15:14:13.726489
-
-"""
-from alembic import op
-import sqlalchemy as sa
-from sqlalchemy.dialects import sqlite
-
-# revision identifiers, used by Alembic.
-revision = 'aac569c672de'
-down_revision = '64fec6271a50'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    # op.create_table('_artic_samples',
-    # sa.Column('id', sa.INTEGER(), nullable=False),
-    # sa.Column('well_number', sa.String(length=8), nullable=True),
-    # sa.Column('rsl_plate_id', sa.INTEGER(), nullable=True),
-    # sa.Column('ww_sample_full_id', sa.String(length=64), nullable=False),
-    # sa.Column('lims_sample_id', sa.String(length=64), nullable=False),
-    # sa.Column('ct_1', sa.FLOAT(precision=2), nullable=True),
-    # sa.Column('ct_2', sa.FLOAT(precision=2), nullable=True),
-    # sa.ForeignKeyConstraint(['rsl_plate_id'], ['_submissions.id'], name='fk_WWA_submission_id', ondelete='SET NULL'),
-    # sa.PrimaryKeyConstraint('id')
-    # )
-    op.drop_table('_alembic_tmp__submissions')
-    
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.create_table('_alembic_tmp__submissions',
-    sa.Column('id', sa.INTEGER(), nullable=False),
-    sa.Column('rsl_plate_num', sa.VARCHAR(length=32), nullable=False),
-    sa.Column('submitter_plate_num', sa.VARCHAR(length=127), nullable=True),
-    sa.Column('submitted_date', sa.TIMESTAMP(), nullable=True),
-    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.VARCHAR(length=32), nullable=True),
-    sa.Column('technician', sa.VARCHAR(length=64), nullable=True),
-    sa.Column('reagents_id', sa.VARCHAR(), nullable=True),
-    sa.Column('extraction_info', sqlite.JSON(), nullable=True),
-    sa.Column('run_cost', sa.FLOAT(), nullable=True),
-    sa.Column('uploaded_by', sa.VARCHAR(length=32), nullable=True),
-    sa.Column('pcr_info', sqlite.JSON(), nullable=True),
-    sa.Column('comment', sqlite.JSON(), nullable=True),
-    sa.ForeignKeyConstraint(['extraction_kit_id'], ['_kits.id'], ondelete='SET NULL'),
-    sa.ForeignKeyConstraint(['reagents_id'], ['_reagents.id'], ondelete='SET NULL'),
-    sa.ForeignKeyConstraint(['submitting_lab_id'], ['_organizations.id'], ondelete='SET NULL'),
-    sa.PrimaryKeyConstraint('id'),
-    sa.UniqueConstraint('rsl_plate_num'),
-    sa.UniqueConstraint('submitter_plate_num')
-    )
-    # op.drop_table('_artic_samples')
-    # ### end Alembic commands ###
--- a/alembic/versions/afbdd9e46207_add_extraction_info_to_submissions.py
+++ b/alembic/versions/afbdd9e46207_add_extraction_info_to_submissions.py
@@ -1,40 +0,0 @@
-"""add extraction info to submissions
-
-Revision ID: afbdd9e46207
-Revises: 8753ed70f148
-Create Date: 2023-01-30 13:05:42.858306
-
-"""
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = 'afbdd9e46207'
-down_revision = '8753ed70f148'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_contacts', schema=None) as batch_op:
-        batch_op.add_column(sa.Column('organization_id', sa.INTEGER(), nullable=True))
-        batch_op.create_foreign_key('fk_contact_org_id', '_organizations', ['organization_id'], ['id'], ondelete='SET NULL')
-
-    with op.batch_alter_table('_submissions', schema=None) as batch_op:
-        batch_op.add_column(sa.Column('extraction_info', sa.JSON(), nullable=True))
-
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_submissions', schema=None) as batch_op:
-        batch_op.drop_column('extraction_info')
-
-    with op.batch_alter_table('_contacts', schema=None) as batch_op:
-        batch_op.drop_constraint('fk_contact_org_id', type_='foreignkey')
-        batch_op.drop_column('organization_id')
-
-    # ### end Alembic commands ###
--- a/alembic/versions/cc9672a505f5_added_discount_table.py
+++ b/alembic/versions/cc9672a505f5_added_discount_table.py
@@ -1,37 +0,0 @@
-"""added discount table
-
-Revision ID: cc9672a505f5
-Revises: 00de69ad6eab
-Create Date: 2023-04-27 12:58:41.331563
-
-"""
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision = 'cc9672a505f5'
-down_revision = '00de69ad6eab'
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.create_table('_discounts',
-    sa.Column('id', sa.INTEGER(), nullable=False),
-    sa.Column('kit_id', sa.INTEGER(), nullable=True),
-    sa.Column('client_id', sa.INTEGER(), nullable=True),
-    sa.Column('amount', sa.FLOAT(precision=2), nullable=True),
-    sa.ForeignKeyConstraint(['client_id'], ['_organizations.id'], name='fk_org_id', ondelete='SET NULL'),
-    sa.ForeignKeyConstraint(['kit_id'], ['_kits.id'], name='fk_kit_type_id', ondelete='SET NULL'),
-    sa.PrimaryKeyConstraint('id')
-    )
-    
-    # ### end Alembic commands ###
-
-
-def downgrade() -> None:
-    # ### commands auto generated by Alembic - please adjust! ###
-    op.drop_table('_discounts')
-    # ### end Alembic commands ###