Pending large code cleanup

2024-01-31 15:21:07 -06:00
parent 319f72cab2
commit eda62fba5a
19 changed files with 741 additions and 103 deletions
--- a/src/submissions/backend/validators/init.py
+++ b/src/submissions/backend/validators/init.py
@@ -3,6 +3,7 @@ from pathlib import Path
 from openpyxl import load_workbook
 from backend.db.models import BasicSubmission, SubmissionType
 from datetime import date
+from tools import jinja_template_loading

 logger = logging.getLogger(f"submissions.{__name__}")

@@ -126,9 +127,20 @@ class RSLNamer(object):
                today = parse(today.group())
            except AttributeError:
                today = datetime.now()
-        previous = BasicSubmission.query(start_date=today, end_date=today, submission_type=data['submission_type'])
-        plate_number = len(previous) + 1
+        if "rsl_plate_num" in data.keys():
+            plate_number = data['rsl_plate_num'].split("-")[-1][0]
+        else:
+            previous = BasicSubmission.query(start_date=today, end_date=today, submission_type=data['submission_type'])
+            plate_number = len(previous) + 1
        return f"RSL-{data['abbreviation']}-{today.year}{str(today.month).zfill(2)}{str(today.day).zfill(2)}-{plate_number}"
+    
+    @classmethod
+    def construct_export_name(cls, template, **kwargs):
+        logger.debug(f"Kwargs: {kwargs}")
+        logger.debug(f"Template: {template}")
+        environment = jinja_template_loading()
+        template = environment.from_string(template)
+        return template.render(**kwargs)

        
 from .pydant import *
--- a/src/submissions/backend/validators/pydant.py
+++ b/src/submissions/backend/validators/pydant.py
@@ -8,7 +8,7 @@ from pydantic import BaseModel, field_validator, Field
 from datetime import date, datetime, timedelta
 from dateutil.parser import parse
 from dateutil.parser._parser import ParserError
-from typing import List, Any, Tuple
+from typing import List, Tuple
 from . import RSLNamer
 from pathlib import Path
 from tools import check_not_nan, convert_nans_to_nones, jinja_template_loading, Report, Result, row_map
@@ -156,8 +156,9 @@ class PydSample(BaseModel, extra='allow'):
    sample_type: str
    row: int|List[int]|None
    column: int|List[int]|None
+    assoc_id: int|List[int]|None = Field(default=None)

-    @field_validator("row", "column")
+    @field_validator("row", "column", "assoc_id")
    @classmethod
    def row_int_to_list(cls, value):
        if isinstance(value, int):
@@ -193,14 +194,14 @@ class PydSample(BaseModel, extra='allow'):
        out_associations = []
        if submission != None:
            assoc_type = self.sample_type.replace("Sample", "").strip()
-            for row, column in zip(self.row, self.column):
-                # logger.debug(f"Looking up association with identity: ({submission.submission_type_name} Association)")
+            for row, column, id in zip(self.row, self.column, self.assoc_id):
+                logger.debug(f"Looking up association with identity: ({submission.submission_type_name} Association)")
                logger.debug(f"Looking up association with identity: ({assoc_type} Association)")
                association = SubmissionSampleAssociation.query_or_create(association_type=f"{assoc_type} Association", 
-                                                                          submission=submission, 
-                                                                          sample=instance, 
-                                                                          row=row, column=column)
-                logger.debug(f"Using submission_sample_association: {association}")
+                                                                            submission=submission, 
+                                                                            sample=instance, 
+                                                                            row=row, column=column, id=id)
+                # logger.debug(f"Using submission_sample_association: {association}")
                try:
                    instance.sample_submission_associations.append(association)
                    out_associations.append(association)
@@ -254,7 +255,7 @@ class PydEquipment(BaseModel, extra='ignore'):
            assoc.process = process
            assoc.role = self.role
            # equipment.equipment_submission_associations.append(assoc)
-            equipment.equipment_submission_associations.append(assoc)
+            # equipment.equipment_submission_associations.append(assoc)
        else:
            assoc = None
        return equipment, assoc
@@ -275,7 +276,7 @@ class PydSubmission(BaseModel, extra='allow'):
    comment: dict|None = Field(default=dict(value="", missing=True), validate_default=True)
    reagents: List[dict]|List[PydReagent] = []
    samples: List[PydSample]
-    equipment: List[PydEquipment]|None
+    equipment: List[PydEquipment]|None =[]

    @field_validator('equipment', mode='before')
    @classmethod
@@ -421,6 +422,16 @@ class PydSubmission(BaseModel, extra='allow'):
            value['value'] = values.data['submission_type']['value']
        return value

+    @field_validator("samples")
+    def assign_ids(cls, value, values):
+        starting_id = SubmissionSampleAssociation.autoincrement_id()
+        output = []
+        for iii, sample in enumerate(value, start=starting_id):
+            sample.assoc_id = [iii]
+            output.append(sample)
+        return output
+
+
    def handle_duplicate_samples(self):
        """
        Collapses multiple samples with same submitter id into one with lists for rows, columns.
@@ -428,14 +439,19 @@ class PydSubmission(BaseModel, extra='allow'):
        """        
        submitter_ids = list(set([sample.submitter_id for sample in self.samples]))
        output = []
-        for id in submitter_ids:
+        for iii, id in enumerate(submitter_ids, start=1):
            relevants = [item for item in self.samples if item.submitter_id==id]
            if len(relevants) <= 1:
                output += relevants
            else:
                rows = [item.row[0] for item in relevants]
                columns = [item.column[0] for item in relevants]
+                ids = [item.assoc_id[0] for item in relevants]
+                # for jjj, rel in enumerate(relevants, start=1):
+                #     starting_id += jjj  
+                #     ids.append(starting_id)                  
                dummy = relevants[0]
+                dummy.assoc_id = ids
                dummy.row = rows
                dummy.column = columns
                output.append(dummy)
@@ -663,14 +679,17 @@ class PydSubmission(BaseModel, extra='allow'):
        logger.debug(f"Workbook sheets: {workbook.sheetnames}")
        worksheet = workbook[sample_info["lookup_table"]['sheet']]
        samples = sorted(self.samples, key=attrgetter('column', 'row'))
-        custom_sampler = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type).adjust_autofill_samples
-        samples = custom_sampler(samples=samples)
+        submission_obj = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
+        samples = submission_obj.adjust_autofill_samples(samples=samples)
        logger.debug(f"Samples: {pformat(samples)}")
        # Fail safe against multiple instances of the same sample
        for iii, sample in enumerate(samples, start=1):
-            row = sample_info['lookup_table']['start_row'] + iii
+            logger.debug(f"Sample: {sample}")
+            row = submission_obj.custom_sample_autofill_row(sample, worksheet=worksheet)
+            logger.debug(f"Writing to {row}")
+            if row == None:
+                row = sample_info['lookup_table']['start_row'] + iii
            fields = [field for field in list(sample.model_fields.keys()) + list(sample.model_extra.keys()) if field in sample_info['sample_columns'].keys()]
-            
            for field in fields:
                column = sample_info['sample_columns'][field]
                value = getattr(sample, field)