WastewaterArcticAssociation completed.

alembic/versions/16b20d4368e6_made_wastewaterarticassociation.py

@@ -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 ###

alembic/versions/861b52a2004e_adding_fields_to_artic.py

@@ -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 ###

alembic/versions/874af342c82c_adding_ranking_to_.py

@@ -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 ###

alembic/versions/a04c25fd9138_splitting_off_sample_info_in_.py

@@ -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 ###

alembic/versions/b744e8a452fd_attaching_contact_to_submission.py

@@ -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 ###

alembic/versions/d2b094cfa308_adding_tips.py

@@ -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 ###

alembic/versions/f829a8ab292f_adding_configitems_to_db.py

@@ -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 ###

src/submissions/backend/db/models/submissions.py

@@ -1789,28 +1789,28 @@ class WastewaterArtic(BasicSubmission):
         """
         # logger.debug(f"Hello from {self.__class__.__name__} dictionary sample adjuster.")
         output = []
-        set_plate = None
+        # set_plate = None
         for assoc in self.submission_sample_associations:
             dicto = assoc.to_sub_dict()
-            if self.source_plates is None:
+            # if self.source_plates is None:
-                output.append(dicto)
+            #     output.append(dicto)
-                continue
+            #     continue
-            for item in self.source_plates:
+            # for item in self.source_plates:
-                if assoc.sample.id is None:
+            #     if assoc.sample.id is None:
-                    old_plate = None
+            #         old_plate = None
-                else:
+            #     else:
-                    old_plate = WastewaterAssociation.query(submission=item['plate'], sample=assoc.sample, limit=1)
+            #         old_plate = WastewaterAssociation.query(submission=item['plate'], sample=assoc.sample, limit=1)
-                if old_plate is not None:
+            #     if old_plate is not None:
-                    set_plate = old_plate.submission.rsl_plate_num
+            #         set_plate = old_plate.submission.rsl_plate_num
-                    # logger.debug(f"Dictionary: {pformat(dicto)}")
+            #         # logger.debug(f"Dictionary: {pformat(dicto)}")
-                    if dicto['ww_processing_num'].startswith("NTC"):
+            #         if dicto['ww_processing_num'].startswith("NTC"):
-                        dicto['well'] = dicto['ww_processing_num']
+            #             dicto['well'] = dicto['ww_processing_num']
-                    else:
+            #         else:
-                        dicto['well'] = f"{row_map[old_plate.row]}{old_plate.column}"
+            #             dicto['well'] = f"{row_map[old_plate.row]}{old_plate.column}"
-                    break
+            #         break
-                elif dicto['ww_processing_num'].startswith("NTC"):
+            #     elif dicto['ww_processing_num'].startswith("NTC"):
-                    dicto['well'] = dicto['ww_processing_num']
+            #         dicto['well'] = dicto['ww_processing_num']
-            dicto['plate_name'] = set_plate
+            # dicto['plate_name'] = set_plate
             # logger.debug(f"Here is our raw sample: {pformat(dicto)}")
             output.append(dicto)
         return output
@@ -2342,7 +2342,7 @@ class SubmissionSampleAssociation(BaseClass):
     }
 
     def __init__(self, submission: BasicSubmission = None, sample: BasicSample = None, row: int = 1, column: int = 1,
-                 id: int | None = None, submission_rank: int = 0):
+                 id: int | None = None, submission_rank: int = 0, **kwargs):
         self.submission = submission
         self.sample = sample
         self.row = row
@@ -2352,6 +2352,12 @@ class SubmissionSampleAssociation(BaseClass):
             self.id = id
         else:
             self.id = self.__class__.autoincrement_id()
+        logger.debug(f"Looking at kwargs: {pformat(kwargs)}")
+        for k,v in kwargs.items():
+            try:
+                self.__setattr__(k, v)
+            except AttributeError:
+                logger.error(f"Couldn't set {k} to {v}")
         # logger.debug(f"Using submission sample association id: {self.id}")
 
     def __repr__(self) -> str:
@@ -2532,7 +2538,7 @@ class SubmissionSampleAssociation(BaseClass):
        Returns:
             SubmissionSampleAssociation: Queried or new association.
         """
-        # logger.debug(f"Attempting create or query with {kwargs}")
+        logger.debug(f"Attempting create or query with {kwargs}")
         match submission:
             case BasicSubmission():
                 pass
@@ -2562,7 +2568,6 @@ class SubmissionSampleAssociation(BaseClass):
         if instance is None:
             # sanitized_kwargs = {k:v for k,v in kwargs.items() if k not in ['id']}
             used_cls = cls.find_polymorphic_subclass(polymorphic_identity=association_type)
-            # instance = used_cls(submission=submission, sample=sample, id=id, **kwargs)
             instance = used_cls(submission=submission, sample=sample, id=id, **kwargs)
         return instance
 
@@ -2627,3 +2632,48 @@ class WastewaterAssociation(SubmissionSampleAssociation):
         except ValueError as e:
             logger.error(f"Problem incrementing id: {e}")
             return 1
+
+
+class WastewaterArticAssociation(SubmissionSampleAssociation):
+
+    id = Column(INTEGER, ForeignKey("_submissionsampleassociation.id"), primary_key=True)
+    source_plate = Column(String(16))
+    source_plate_number = Column(INTEGER)
+    source_well = Column(String(8))
+    ct = Column(String(8))  #: AKA ct for N1
+
+    __mapper_args__ = dict(polymorphic_identity="Wastewater Artic Association",
+                           polymorphic_load="inline",
+                           inherit_condition=(id == SubmissionSampleAssociation.id))
+
+    def to_sub_dict(self) -> dict:
+        """
+        Returns a sample dictionary updated with instance information. Extends parent
+
+        Returns:
+            dict: Updated dictionary with row, column and well updated
+        """
+
+        sample = super().to_sub_dict()
+        sample['ct'] = self.ct
+        sample['source_plate'] = self.source_plate
+        sample['source_plate_number'] = self.source_plate_number
+        sample['source_well'] = self.source_well
+        return sample
+
+    @classmethod
+    def autoincrement_id(cls) -> int:
+        """
+        Increments the association id automatically. Overrides parent
+
+        Returns:
+            int: incremented id
+        """
+        try:
+            parent = [base for base in cls.__bases__ if base.__name__ == "SubmissionSampleAssociation"][0]
+            return max([item.id for item in parent.query()]) + 1
+        except ValueError as e:
+            logger.error(f"Problem incrementing id: {e}")
+            return 1
+
+

src/submissions/backend/validators/pydant.py

@@ -256,7 +256,7 @@ class PydSample(BaseModel, extra='allow'):
                                                                           submission=submission,
                                                                           sample=instance,
                                                                           row=row, column=column, id=aid,
-                                                                          submission_rank=submission_rank)
+                                                                          submission_rank=submission_rank, **self.model_extra)
                 logger.debug(f"Using submission_sample_association: {association}")
                 try:
                     # instance.sample_submission_associations.append(association)
@@ -375,6 +375,7 @@ class PydSubmission(BaseModel, extra='allow'):
     @classmethod
     def convert_equipment_dict(cls, value):
         # logger.debug(f"Equipment: {value}")
+
         if isinstance(value, dict):
             return value['value']
         return value
@@ -697,6 +698,8 @@ class PydSubmission(BaseModel, extra='allow'):
         for key, value in dicto.items():
             if isinstance(value, dict):
                 value = value['value']
+            if value is None:
+                continue
             # logger.debug(f"Setting {key} to {value}")
             match key:
                 case "reagents":