Working new version.

2023-09-11 13:45:10 -05:00
parent e0b80f6c7a
commit 5a978c9bff
15 changed files with 417 additions and 743 deletions
--- a/src/submissions/frontend/all_window_functions.py
+++ b/src/submissions/frontend/all_window_functions.py
@@ -28,6 +28,8 @@ def select_open_file(obj:QMainWindow, file_extension:str) -> Path:
    except FileNotFoundError:
        home_dir = Path.home().resolve().__str__()
    fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = f"{file_extension}(*.{file_extension})")[0])
+    # fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', filter = f"{file_extension}(*.{file_extension})")[0])
+
    return fname

 def select_save_file(obj:QMainWindow, default_name:str, extension:str) -> Path:
@@ -48,6 +50,8 @@ def select_save_file(obj:QMainWindow, default_name:str, extension:str) -> Path:
    except FileNotFoundError:
        home_dir = Path.home().joinpath(default_name).resolve().__str__()
    fname = Path(QFileDialog.getSaveFileName(obj, "Save File", home_dir, filter = f"{extension}(*.{extension})")[0])
+    # fname = Path(QFileDialog.getSaveFileName(obj, "Save File", filter = f"{extension}(*.{extension})")[0])
+
    return fname

 def extract_form_info(object) -> dict:
--- a/src/submissions/frontend/custom_widgets/sub_details.py
+++ b/src/submissions/frontend/custom_widgets/sub_details.py
@@ -17,6 +17,7 @@ from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
 from PyQt6.QtGui import QAction, QCursor, QPixmap, QPainter
 from backend.db import submissions_to_df, lookup_submission_by_id, delete_submission_by_id, lookup_submission_by_rsl_num, hitpick_plate
 from backend.excel import make_hitpicks
+from tools import check_if_app
 from tools import jinja_template_loading
 from xhtml2pdf import pisa
 from pathlib import Path
@@ -291,10 +292,14 @@ class SubmissionDetails(QDialog):
        # interior.resize(w,900)
        # txt_editor.setText(text)
        # interior.setWidget(txt_editor)
-        self.base_dict['barcode'] = base64.b64encode(make_plate_barcode(self.base_dict['Plate Number'], width=120, height=30)).decode('utf-8')
+        logger.debug(f"Creating barcode.")
+        if not check_if_app():
+            self.base_dict['barcode'] = base64.b64encode(make_plate_barcode(self.base_dict['Plate Number'], width=120, height=30)).decode('utf-8')
        sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=self.base_dict['Plate Number'])
        # plate_dicto = hitpick_plate(sub)
+        logger.debug(f"Hitpicking plate...")
        plate_dicto = sub.hitpick_plate()
+        logger.debug(f"Making platemap...")
        platemap = make_plate_map(plate_dicto)
        logger.debug(f"platemap: {platemap}")
        image_io = BytesIO()
--- a/src/submissions/frontend/main_window_functions.py
+++ b/src/submissions/frontend/main_window_functions.py
@@ -25,7 +25,7 @@ from backend.db.functions import (
    lookup_all_orgs, lookup_kittype_by_use, lookup_kittype_by_name, 
    construct_submission_info, lookup_reagent, store_submission, lookup_submissions_by_date_range, 
    create_kit_from_yaml, create_org_from_yaml, get_control_subtypes, get_all_controls_by_type,
-    lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num, update_ww_sample,
+    lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num, update_subsampassoc_with_pcr,
    check_kit_integrity
 )
 from backend.excel.parser import SheetParser, PCRParser
@@ -133,7 +133,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
                # lookup existing kits by 'submission_type' decided on by sheetparser
                # uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_by=pyd.submission_type['value'].lower())]
                logger.debug(f"Looking up kits used for {pyd.submission_type['value']}")
-                uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_by=pyd.submission_type['value'])]
+                uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_for=pyd.submission_type['value'])]
                logger.debug(f"Kits received for {pyd.submission_type['value']}: {uses}")
                if check_not_nan(value['value']):
                    logger.debug(f"The extraction kit in parser was: {value['value']}")
@@ -365,7 +365,7 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
    if kit_integrity != None:
        return obj, dict(message=kit_integrity['message'], status="critical")
    logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
-    result = store_submission(ctx=obj.ctx, base_submission=base_submission, samples=obj.samples)
+    result = store_submission(ctx=obj.ctx, base_submission=base_submission)
    # check result of storing for issues
    # update summary sheet
    obj.table_widget.sub_wid.setData()
@@ -383,7 +383,8 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
        excel_map = extraction_kit.construct_xl_map_for_use(obj.current_submission_type)
        logger.debug(f"Extraction kit map:\n\n{pprint.pformat(excel_map)}")
        # excel_map.update(extraction_kit.used_for[obj.current_submission_type.replace('_', ' ').title()])
-        input_reagents = [item.to_reagent_dict() for item in parsed_reagents]
+        input_reagents = [item.to_reagent_dict(extraction_kit=base_submission.extraction_kit) for item in parsed_reagents]
+        logger.debug(f"Parsed reagents going into autofile: {pprint.pformat(input_reagents)}")
        autofill_excel(obj=obj, xl_map=excel_map, reagents=input_reagents, missing_reagents=obj.missing_reagents, info=info, missing_info=obj.missing_info)
    if hasattr(obj, 'csv'):
        dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
@@ -844,10 +845,16 @@ def import_pcr_results_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
    obj.ctx.database_session.commit()
    logger.debug(f"Got {len(parser.samples)} samples to update!")
    logger.debug(f"Parser samples: {parser.samples}")
-    for sample in parser.samples:
-        logger.debug(f"Running update on: {sample['sample']}")
-        sample['plate_rsl'] = sub.rsl_plate_num
-        update_ww_sample(ctx=obj.ctx, sample_obj=sample)
+    for sample in sub.samples:
+        logger.debug(f"Running update on: {sample}")
+        try:
+            sample_dict = [item for item in parser.samples if item['sample']==sample.rsl_number][0]
+        except IndexError:
+            continue
+        # sample['plate_rsl'] = sub.rsl_plate_num
+        # update_ww_sample(ctx=obj.ctx, sample_obj=sample)
+        update_subsampassoc_with_pcr(ctx=obj.ctx, submission=sub, sample=sample, input_dict=sample_dict)
+
    result = dict(message=f"We added PCR info to {sub.rsl_plate_num}.", status='information')
    return obj, result

@@ -872,7 +879,16 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
    # pare down the xl map to only the missing data.
    relevant_reagent_map = {k:v for k,v in xl_map.items() if k in [reagent.type for reagent in missing_reagents]}
    # pare down reagents to only what's missing
+    logger.debug(f"Checking {[item['type'] for item in reagents]} against {[reagent.type for reagent in missing_reagents]}")
    relevant_reagents = [item for item in reagents if item['type'] in [reagent.type for reagent in missing_reagents]]
+    # relevant_reagents = []
+    # for item in reagents:
+    #     logger.debug(f"Checking {item['type']} in {[reagent.type for reagent in missing_reagents]}")
+    #     if item['type'] in [reagent.type for reagent in missing_reagents]:
+    #         logger.debug("Hit!")
+    #         relevant_reagents.append(item)
+    #     else:
+    #         logger.debug('Miss.')
    logger.debug(f"Here are the relevant reagents: {pprint.pformat(relevant_reagents)}")
    # hacky manipulation of submission type so it looks better.
    # info['submission_type'] = info['submission_type'].replace("_", " ").title()