Pre-reagent/submission association update.

CHANGELOG.md

@@ -1,5 +1,6 @@
 ## 202312.01
 
+- Control samples info now available in plate map.
 - Backups will now create an regenerated xlsx file.
 - Report generator now does sums automatically.
 

TODO.md

@@ -27,7 +27,7 @@
     - Should be used when coming in to parser and when leaving form. NO OTHER PLACES.
 - [x] Change 'check_is_power_user' to decorator.
 - [x] Drag and drop files into submission form area?
-- [ ] Get info for controls into their sample hitpicks.
+- [x] Get info for controls into their sample hitpicks.
 - [x] Move submission-type specific parser functions into class methods in their respective models.
 - [x] Improve function results reporting.
     - Maybe make it a list until it gets to the reporter?

alembic.ini

@@ -57,7 +57,7 @@ version_path_separator = os  # Use os.pathsep. Default configuration used for ne
 
 ; sqlalchemy.url = sqlite:///L:\Robotics Laboratory Support\Submissions\submissions.db
 ; sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\Submissions_app_backups\DB_backups\submissions-new.db
-; sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\python\submissions\tests\test_assets\submissions-test.db
+sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\python\submissions\tests\test_assets\submissions-test.db
 
 
 [post_write_hooks]

alembic/versions/2684f065037c_link_controls_with_bacterial_culture_.py

@@ -0,0 +1,34 @@
+"""link controls with Bacterial Culture Samples
+
+Revision ID: 2684f065037c
+Revises: 7e7b6eeca468
+Create Date: 2023-12-05 10:29:31.126732
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '2684f065037c'
+down_revision = '7e7b6eeca468'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('_control_samples', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('sample_id', sa.INTEGER(), nullable=True))
+        batch_op.create_foreign_key('cont_BCS_id', '_samples', ['sample_id'], ['id'], ondelete='SET NULL')
+
+    # ### 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_constraint('cont_BCS_id', type_='foreignkey')
+        batch_op.drop_column('sample_id')
+
+    # ### end Alembic commands ###

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

@@ -71,6 +71,8 @@ class Control(BaseClass):
     refseq_version = Column(String(16)) #: version of refseq used in fastq parsing
     kraken2_version = Column(String(16)) #: version of kraken2 used in fastq parsing
     kraken2_db_version = Column(String(32)) #: folder name of kraken2 db
+    sample = relationship("BacterialCultureSample", back_populates="control")
+    sample_id = Column(INTEGER, ForeignKey("_samples.id", ondelete="SET NULL", name="cont_BCS_id"))
 
     def __repr__(self) -> str:
         return f"<Control({self.name})>"
@@ -243,3 +245,8 @@ class Control(BaseClass):
             case _:
                 pass
         return query_return(query=query, limit=limit)
+
+    def save(self):
+        self.__database_session__.add(self)
+        self.__database_session__.commit()
+

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

@@ -58,7 +58,7 @@ class BasicSubmission(BaseClass):
     run_cost = Column(FLOAT(2)) #: total cost of running the plate. Set from constant and mutable kit costs at time of creation.
     uploaded_by = Column(String(32)) #: user name of person who submitted the submission to the database.
     comment = Column(JSON) #: user notes
-    submission_category = Column(String(64)) #: ["Research", "Diagnostic", "Surveillance"], else defaults to submission_type_name
+    submission_category = Column(String(64)) #: ["Research", "Diagnostic", "Surveillance", "Validation"], else defaults to submission_type_name
 
     submission_sample_associations = relationship(
         "SubmissionSampleAssociation",
@@ -1483,6 +1483,7 @@ class BacterialCultureSample(BasicSample):
     # id = Column(INTEGER, ForeignKey('basicsample.id'), primary_key=True)
     organism = Column(String(64)) #: bacterial specimen
     concentration = Column(String(16)) #: sample concentration
+    control = relationship("Control", back_populates="sample", uselist=False)
     __mapper_args__ = {"polymorphic_identity": "Bacterial Culture Sample", "polymorphic_load": "inline"}
 
     def to_sub_dict(self, submission_rsl:str) -> dict:
@@ -1496,6 +1497,13 @@ class BacterialCultureSample(BasicSample):
         sample['name'] = f"{self.submitter_id} - ({self.organism})"
         return sample
 
+    def to_hitpick(self, submission_rsl: str | None = None) -> dict | None:
+        sample = super().to_hitpick(submission_rsl)
+        if self.control != None:
+            sample['colour'] = [0,128,0]
+            sample['tooltip'] += f"<br>- Control: {self.control.controltype.name} - {self.control.controltype.targets}"
+        return sample
+
 # Submission to Sample Associations
 
 class SubmissionSampleAssociation(BaseClass):

src/submissions/backend/validators/pydant.py

@@ -325,7 +325,7 @@ class PydSubmission(BaseModel, extra='allow'):
     @field_validator("submission_category")
     @classmethod
     def rescue_category(cls, value, values):
-        if value['value'] not in ["Research", "Diagnostic", "Surveillance"]:
+        if value['value'] not in ["Research", "Diagnostic", "Surveillance", "Validation"]:
             value['value'] = values.data['submission_type']['value']
         return value
 

src/submissions/frontend/visualizations/plate_map.py

@@ -31,10 +31,14 @@ def make_plate_map(sample_list:list) -> Image:
     # Go through samples and change its row/column to red if positive, else blue
     for sample in sample_list:
         logger.debug(f"sample keys: {list(sample.keys())}")
+        # set color of square
         if sample['positive']:
             colour = [255,0,0]
         else:
-            colour = [0,0,255]
+            if 'colour' in sample.keys():
+                colour = sample['colour']
+            else:
+                colour = [0,0,255]
         grid[int(sample['row'])-1][int(sample['column'])-1] = colour
     # Create pixel image from the grid and enlarge
     img = Image.fromarray(grid).resize((1200, 800), resample=Image.NEAREST)
@@ -99,7 +103,10 @@ def make_plate_map_html(sample_list:list, plate_rows:int=8, plate_columns=12) ->
         if sample['positive']:
             sample['background_color'] = "#f10f07"
         else:
-            sample['background_color'] = "#80cbc4"
+            if "colour" in sample.keys():
+                sample['background_color'] = "#69d84f"
+            else:
+                sample['background_color'] = "#80cbc4"
     output_samples = []
     for column in range(1, plate_columns+1):
         for row in range(1, plate_rows+1):