landon/Submissions-App
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Before making a big mistake.

Browse Source
This commit is contained in:
Landon Wark
2023-11-16 14:55:55 -06:00
parent 6e865f1551
commit 74957ee318
22 changed files with 137 additions and 924 deletions
Download Patch File Download Diff File Expand all files Collapse all files

34
alembic/versions/3d9a88bd4ecd_added_in_other_ww_techs.py
View File

@@ -1,34 +0,0 @@
"""added in other ww techs
Revision ID: 3d9a88bd4ecd
Revises: f7f46e72f057
Create Date: 2023-08-30 11:03:41.575219
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '3d9a88bd4ecd'
down_revision = 'f7f46e72f057'
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('ext_technician', sa.String(length=64), nullable=True))
batch_op.add_column(sa.Column('pcr_technician', sa.String(length=64), 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_technician')
batch_op.drop_column('ext_technician')
# ### end Alembic commands ###

32
alembic/versions/8a5bc2924ef9_adding_artic_technician_to_artic.py
View File

@@ -1,32 +0,0 @@
"""adding artic_technician to Artic
Revision ID: 8a5bc2924ef9
Revises: b95478ffb4a3
Create Date: 2023-10-31 13:59:47.746122
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '8a5bc2924ef9'
down_revision = 'b95478ffb4a3'
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('artic_technician', sa.String(length=64), 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('artic_technician')
# ### end Alembic commands ###

33
alembic/versions/9a133efb3ffd_adjusting_reagents_reagenttypes_to_many_.py
View File

@@ -1,33 +0,0 @@
"""adjusting reagents/reagenttypes to many-to-many
Revision ID: 9a133efb3ffd
Revises: 3d9a88bd4ecd
Create Date: 2023-09-01 10:28:22.335890
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '9a133efb3ffd'
down_revision = '3d9a88bd4ecd'
branch_labels = None
depends_on = None
def upgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
op.create_table('_reagenttypes_reagents',
sa.Column('reagent_id', sa.INTEGER(), nullable=True),
sa.Column('reagenttype_id', sa.INTEGER(), nullable=True),
sa.ForeignKeyConstraint(['reagent_id'], ['_reagents.id'], ),
sa.ForeignKeyConstraint(['reagenttype_id'], ['_reagent_types.id'], )
)
# ### end Alembic commands ###
def downgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
op.drop_table('_reagenttypes_reagents')
# ### end Alembic commands ###

32
alembic/versions/b95478ffb4a3_adding_submission_category.py
View File

@@ -1,32 +0,0 @@
"""adding submission category
Revision ID: b95478ffb4a3
Revises: 9a133efb3ffd
Create Date: 2023-10-03 14:00:09.663055
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = 'b95478ffb4a3'
down_revision = '9a133efb3ffd'
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('submission_category', sa.String(length=64), 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('submission_category')
# ### end Alembic commands ###

204
alembic/versions/f7f46e72f057_rebuild_database.py
View File

@@ -1,204 +0,0 @@
"""rebuild database
Revision ID: f7f46e72f057
Revises:
Create Date: 2023-08-30 09:47:18.071070
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = 'f7f46e72f057'
down_revision = None
branch_labels = None
depends_on = None
def upgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
op.create_table('_contacts',
sa.Column('id', sa.INTEGER(), nullable=False),
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.PrimaryKeyConstraint('id')
)
op.create_table('_control_types',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('name', sa.String(length=255), nullable=True),
sa.Column('targets', sa.JSON(), nullable=True),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('name')
)
op.create_table('_kits',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('name', sa.String(length=64), nullable=True),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('name')
)
op.create_table('_organizations',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('name', sa.String(length=64), nullable=True),
sa.Column('cost_centre', sa.String(), nullable=True),
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('eol_ext', sa.Interval(), nullable=True),
sa.Column('last_used', sa.String(length=32), nullable=True),
sa.PrimaryKeyConstraint('id')
)
op.create_table('_samples',
sa.Column('id', sa.INTEGER(), nullable=False),
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('received_date', sa.TIMESTAMP(), nullable=True),
sa.Column('notes', sa.String(length=2000), 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),
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),
sa.Column('name', sa.String(length=64), nullable=True),
sa.Column('lot', sa.String(length=64), nullable=True),
sa.Column('expiry', sa.TIMESTAMP(), nullable=True),
sa.ForeignKeyConstraint(['type_id'], ['_reagent_types.id'], name='fk_reagent_type_id', ondelete='SET NULL'),
sa.PrimaryKeyConstraint('id')
)
op.create_table('_reagenttypes_kittypes',
sa.Column('reagent_types_id', sa.INTEGER(), nullable=False),
sa.Column('kits_id', sa.INTEGER(), nullable=False),
sa.Column('uses', sa.JSON(), nullable=True),
sa.Column('required', sa.INTEGER(), nullable=True),
sa.ForeignKeyConstraint(['kits_id'], ['_kits.id'], ),
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),
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),
sa.Column('sample_count', sa.INTEGER(), nullable=True),
sa.Column('extraction_kit_id', sa.INTEGER(), 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),
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(['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'),
sa.UniqueConstraint('submitter_plate_num')
)
op.create_table('_control_samples',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('parent_id', sa.String(), nullable=True),
sa.Column('name', sa.String(length=255), nullable=True),
sa.Column('submitted_date', sa.TIMESTAMP(), nullable=True),
sa.Column('contains', sa.JSON(), nullable=True),
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'),
sa.UniqueConstraint('name')
)
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('_submission_sample',
sa.Column('sample_id', sa.INTEGER(), nullable=False),
sa.Column('submission_id', sa.INTEGER(), nullable=False),
sa.Column('row', sa.INTEGER(), nullable=False),
sa.Column('column', sa.INTEGER(), nullable=False),
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('submission_id', 'row', 'column')
)
# ### end Alembic commands ###
def downgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
op.drop_table('_submission_sample')
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')
op.drop_table('_kits')
op.drop_table('_control_types')
op.drop_table('_contacts')
# ### end Alembic commands ###