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

WastewaterArcticAssociation completed.

Browse Source
This commit is contained in:
lwark
2024-06-13 13:47:30 -05:00
parent f73a3e6c35
commit 4a7d0b0bd4
9 changed files with 449 additions and 24 deletions
Download Patch File Download Diff File Expand all files Collapse all files

54
alembic/versions/16b20d4368e6_made_wastewaterarticassociation.py Normal file
View File

@@ -0,0 +1,54 @@
"""Made WastewaterArticAssociation
Revision ID: 16b20d4368e6
Revises: d2b094cfa308
Create Date: 2024-06-13 12:16:48.385516
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '16b20d4368e6'
down_revision = 'd2b094cfa308'
branch_labels = None
depends_on = None
def upgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
op.create_table('_wastewaterarticassociation',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('source_plate', sa.String(length=16), nullable=True),
sa.Column('source_plate_number', sa.INTEGER(), nullable=True),
sa.Column('source_well', sa.String(length=8), nullable=True),
sa.Column('ct', sa.String(length=8), nullable=True),
sa.ForeignKeyConstraint(['id'], ['_submissionsampleassociation.id'], ),
sa.PrimaryKeyConstraint('id')
)
# with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
# batch_op.create_unique_constraint(None, ['id'])
#
# with op.batch_alter_table('_submissiontipsassociation', schema=None) as batch_op:
# batch_op.alter_column('role_name',
# existing_type=sa.INTEGER(),
# type_=sa.String(length=32),
# existing_nullable=True)
# ### end Alembic commands ###
def downgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('_submissiontipsassociation', schema=None) as batch_op:
batch_op.alter_column('role_name',
existing_type=sa.String(length=32),
type_=sa.INTEGER(),
existing_nullable=True)
with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
batch_op.drop_constraint(None, type_='unique')
op.drop_table('_wastewaterarticassociation')
# ### end Alembic commands ###

72
alembic/versions/861b52a2004e_adding_fields_to_artic.py Normal file
View File

@@ -0,0 +1,72 @@
"""Adding fields to Artic
Revision ID: 861b52a2004e
Revises: b744e8a452fd
Create Date: 2024-06-05 13:35:19.012337
"""
from alembic import op
import sqlalchemy as sa
from sqlalchemy.dialects import sqlite
# revision identifiers, used by Alembic.
revision = '861b52a2004e'
down_revision = 'b744e8a452fd'
branch_labels = None
depends_on = None
def upgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
op.drop_table('_alembic_tmp__basicsubmission')
# with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
# batch_op.create_unique_constraint(None, ['id'])
with op.batch_alter_table('_wastewaterartic', schema=None) as batch_op:
batch_op.add_column(sa.Column('artic_date', sa.TIMESTAMP(), nullable=True))
batch_op.add_column(sa.Column('ngs_date', sa.TIMESTAMP(), nullable=True))
batch_op.add_column(sa.Column('gel_date', sa.TIMESTAMP(), nullable=True))
batch_op.add_column(sa.Column('gel_barcode', sa.String(length=16), nullable=True))
# ### end Alembic commands ###
def downgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('_wastewaterartic', schema=None) as batch_op:
batch_op.drop_column('gel_barcode')
batch_op.drop_column('gel_date')
batch_op.drop_column('ngs_date')
batch_op.drop_column('artic_date')
# with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
# batch_op.drop_constraint(None, type_='unique')
op.create_table('_alembic_tmp__basicsubmission',
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_name', sa.VARCHAR(), 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('signed_by', sa.VARCHAR(length=32), nullable=True),
sa.Column('comment', sqlite.JSON(), nullable=True),
sa.Column('submission_category', sa.VARCHAR(length=64), nullable=True),
sa.Column('cost_centre', sa.VARCHAR(length=64), nullable=True),
sa.Column('contact_id', sa.INTEGER(), nullable=True),
sa.ForeignKeyConstraint(['contact_id'], ['_contact.id'], ondelete='SET NULL'),
sa.ForeignKeyConstraint(['extraction_kit_id'], ['_kittype.id'], ondelete='SET NULL'),
sa.ForeignKeyConstraint(['reagents_id'], ['_reagent.id'], ondelete='SET NULL'),
sa.ForeignKeyConstraint(['submission_type_name'], ['_submissiontype.name'], ondelete='SET NULL'),
sa.ForeignKeyConstraint(['submitting_lab_id'], ['_organization.id'], ondelete='SET NULL'),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('rsl_plate_num'),
sa.UniqueConstraint('submitter_plate_num')
)
# ### end Alembic commands ###

34
alembic/versions/874af342c82c_adding_ranking_to_.py Normal file
View File

@@ -0,0 +1,34 @@
"""Adding ranking to SubmissionSampleAssociation
Revision ID: 874af342c82c
Revises: a04c25fd9138
Create Date: 2024-05-03 15:08:20.194275
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '874af342c82c'
down_revision = 'a04c25fd9138'
branch_labels = None
depends_on = None
def upgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
batch_op.add_column(sa.Column('submission_rank', sa.INTEGER(), nullable=False, default=1))
# batch_op.create_unique_constraint(None, ['id'])
# ### end Alembic commands ###
def downgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
# batch_op.drop_constraint(None, type_='unique')
batch_op.drop_column('submission_rank')
# ### end Alembic commands ###

38
alembic/versions/a04c25fd9138_splitting_off_sample_info_in_.py Normal file
View File

@@ -0,0 +1,38 @@
"""splitting off sample info in SubmissionType
Revision ID: a04c25fd9138
Revises: 6d2a357860ef
Create Date: 2024-05-01 09:11:44.957532
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = 'a04c25fd9138'
down_revision = '6d2a357860ef'
branch_labels = None
depends_on = None
def upgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
# with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
# batch_op.create_unique_constraint(None, ['id'])
with op.batch_alter_table('_submissiontype', schema=None) as batch_op:
batch_op.add_column(sa.Column('sample_map', sa.JSON(), nullable=True))
# ### end Alembic commands ###
def downgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('_submissiontype', schema=None) as batch_op:
batch_op.drop_column('sample_map')
# with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
# batch_op.drop_constraint(None, type_='unique')
# ### end Alembic commands ###

40
alembic/versions/b744e8a452fd_attaching_contact_to_submission.py Normal file
View File

@@ -0,0 +1,40 @@
"""Attaching contact to submission
Revision ID: b744e8a452fd
Revises: f829a8ab292f
Create Date: 2024-06-04 14:21:38.163431
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = 'b744e8a452fd'
down_revision = 'f829a8ab292f'
branch_labels = None
depends_on = None
def upgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('_basicsubmission', schema=None) as batch_op:
batch_op.add_column(sa.Column('contact_id', sa.INTEGER(), nullable=True))
batch_op.create_foreign_key('fk_BS_contact_id', '_contact', ['contact_id'], ['id'], ondelete='SET NULL')
# with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
# batch_op.create_unique_constraint(None, ['id'])
# ### end Alembic commands ###
def downgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
# with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
# batch_op.drop_constraint(None, type_='unique')
with op.batch_alter_table('_basicsubmission', schema=None) as batch_op:
batch_op.drop_constraint('fk_BS_contact_id', type_='foreignkey')
batch_op.drop_column('contact_id')
# ### end Alembic commands ###

95
alembic/versions/d2b094cfa308_adding_tips.py Normal file
View File

@@ -0,0 +1,95 @@
"""Adding tips
Revision ID: d2b094cfa308
Revises: 861b52a2004e
Create Date: 2024-06-11 13:16:57.319769
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = 'd2b094cfa308'
down_revision = '861b52a2004e'
branch_labels = None
depends_on = None
def upgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
op.create_table('_tiprole',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('name', sa.String(length=64), nullable=True),
sa.PrimaryKeyConstraint('id')
)
op.create_table('_process_tiprole',
sa.Column('process_id', sa.INTEGER(), nullable=True),
sa.Column('tiprole_id', sa.INTEGER(), nullable=True),
sa.ForeignKeyConstraint(['process_id'], ['_process.id'], ),
sa.ForeignKeyConstraint(['tiprole_id'], ['_tiprole.id'], )
)
op.create_table('_submissiontypetiproleassociation',
sa.Column('tiprole_id', sa.INTEGER(), nullable=False),
sa.Column('submissiontype_id', sa.INTEGER(), nullable=False),
sa.Column('uses', sa.JSON(), nullable=True),
sa.Column('static', sa.INTEGER(), nullable=True),
sa.ForeignKeyConstraint(['submissiontype_id'], ['_submissiontype.id'], ),
sa.ForeignKeyConstraint(['tiprole_id'], ['_tiprole.id'], ),
sa.PrimaryKeyConstraint('tiprole_id', 'submissiontype_id')
)
op.create_table('_tips',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('role_id', sa.INTEGER(), nullable=True),
sa.Column('name', sa.String(length=64), nullable=True),
sa.Column('lot', sa.String(length=64), nullable=True),
sa.ForeignKeyConstraint(['role_id'], ['_tiprole.id'], name='fk_tip_role_id', ondelete='SET NULL'),
sa.PrimaryKeyConstraint('id')
)
op.create_table('_equipment_tips',
sa.Column('equipment_id', sa.INTEGER(), nullable=True),
sa.Column('tips_id', sa.INTEGER(), nullable=True),
sa.ForeignKeyConstraint(['equipment_id'], ['_equipment.id'], ),
sa.ForeignKeyConstraint(['tips_id'], ['_tips.id'], )
)
op.create_table('_submissiontipsassociation',
sa.Column('tip_id', sa.INTEGER(), nullable=False),
sa.Column('submission_id', sa.INTEGER(), nullable=False),
sa.Column('role_name', sa.String(), nullable=True),
sa.ForeignKeyConstraint(['role_name'], ['_tiprole.name'], ),
sa.ForeignKeyConstraint(['submission_id'], ['_submissiontype.id'], ),
sa.ForeignKeyConstraint(['tip_id'], ['_tips.id'], ),
sa.PrimaryKeyConstraint('tip_id', 'submission_id')
)
op.create_table('_tiproles_tips',
sa.Column('tiprole_id', sa.INTEGER(), nullable=True),
sa.Column('tips_id', sa.INTEGER(), nullable=True),
sa.ForeignKeyConstraint(['tiprole_id'], ['_tiprole.id'], ),
sa.ForeignKeyConstraint(['tips_id'], ['_tips.id'], )
)
# op.create_table('_submissions_tips',
# sa.Column('submission_id', sa.INTEGER(), nullable=True),
# sa.Column('tips_id', sa.INTEGER(), nullable=True),
# sa.ForeignKeyConstraint(['submission_id'], ['_basicsubmission.id'], ),
# sa.ForeignKeyConstraint(['tips_id'], ['_tips.id'], )
# )
# with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
# batch_op.create_unique_constraint("unique_ssa_id", ['id'])
# ### end Alembic commands ###
def downgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
# with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
# batch_op.drop_constraint(None, type_='unique')
op.drop_table('_submissions_tips')
op.drop_table('_tiproles_tips')
op.drop_table('_submissiontipassociation')
op.drop_table('_equipment_tips')
op.drop_table('_tips')
op.drop_table('_submissiontypetiproleassociation')
op.drop_table('_process_tiprole')
op.drop_table('_tiprole')
# ### end Alembic commands ###

39
alembic/versions/f829a8ab292f_adding_configitems_to_db.py Normal file
View File

@@ -0,0 +1,39 @@
"""Adding configitems to db
Revision ID: f829a8ab292f
Revises: 874af342c82c
Create Date: 2024-05-15 14:03:11.767480
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = 'f829a8ab292f'
down_revision = '874af342c82c'
branch_labels = None
depends_on = None
def upgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
op.create_table('_configitem',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('key', sa.String(), nullable=True),
sa.Column('value', sa.JSON(), nullable=True),
sa.PrimaryKeyConstraint('id')
)
# with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
# batch_op.create_unique_constraint(None, ['id'])
# ### end Alembic commands ###
def downgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
# with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
# batch_op.drop_constraint(None, type_='unique')
op.drop_table('_configitem')
# ### end Alembic commands ###