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Various bug fixes for new forms.

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This commit is contained in:
Landon Wark
2024-04-25 08:55:32 -05:00
parent 5466c78c3a
commit 8cc161ec56
18 changed files with 520 additions and 218 deletions
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4
CHANGELOG.md
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@@ -1,3 +1,7 @@
## 202404.04
- Storing of default values in db rather than hardcoded.
## 202404.03 ## 202404.03
- Package updates. - Package updates.

7
TODO.md
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@@ -1,4 +1,7 @@
- [ ] Critical: Convert Json lits to dicts so I can have them update properly without using crashy Sqlalchemy-json - [ ] Put "Not applicable" reagents in to_dict() method.
- Currently in to_pydantic().
- [x] Critical: Convert Json lits to dicts so I can have them update properly without using crashy Sqlalchemy-json
- Was actually not necessary.
- [ ] Fix Parsed/Missing mix ups. - [ ] Fix Parsed/Missing mix ups.
- [x] Have sample parser check for controls and add to reagents? - [x] Have sample parser check for controls and add to reagents?
- [x] Update controls to NestedMutableJson - [x] Update controls to NestedMutableJson
@@ -6,7 +9,7 @@
- Possibly due to immutable JSON? But... it's worked before... Right? - Possibly due to immutable JSON? But... it's worked before... Right?
- Based on research, if a top-level JSON field is not changed, SQLalchemy will not detect changes. - Based on research, if a top-level JSON field is not changed, SQLalchemy will not detect changes.
- Using sqlalchemy-json module seems to have helped. - Using sqlalchemy-json module seems to have helped.
- [ ] Add Bead basher and Assit to DB. - [ ] Add Bead basher and Assist to DB.
- [x] Artic not creating right plate name. - [x] Artic not creating right plate name.
- [ ] Merge BasicSubmission.find_subclasses and BasicSubmission.find_polymorphic_subclass - [ ] Merge BasicSubmission.find_subclasses and BasicSubmission.find_polymorphic_subclass
- [x] Fix updating of Extraction Kit in submission form widget. - [x] Fix updating of Extraction Kit in submission form widget.

4
alembic.ini
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@@ -55,9 +55,9 @@ version_path_separator = os # Use os.pathsep. Default configuration used for ne
# are written from script.py.mako # are written from script.py.mako
# output_encoding = utf-8 # output_encoding = utf-8
; sqlalchemy.url = sqlite:///L:\Robotics Laboratory Support\Submissions\submissions.db sqlalchemy.url = sqlite:///L:\Robotics Laboratory Support\Submissions\submissions.db
; sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\Submissions_app_backups\DB_backups\submissions-demo.db ; sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\Submissions_app_backups\DB_backups\submissions-demo.db
sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\python\submissions\mytests\test_assets\submissions-test.db ; sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\python\submissions\mytests\test_assets\submissions-test.db
[post_write_hooks] [post_write_hooks]

51
alembic/versions/6d2a357860ef_adding_cost_centre_storage_to_.py Normal file
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@@ -0,0 +1,51 @@
"""adding cost centre storage to basicsubmission
Revision ID: 6d2a357860ef
Revises: e6647bd661d9
Create Date: 2024-04-24 13:01:14.923814
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '6d2a357860ef'
down_revision = 'e6647bd661d9'
branch_labels = None
depends_on = None
def upgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
# op.drop_table('_alembic_tmp__submissionsampleassociation')
with op.batch_alter_table('_basicsubmission', schema=None) as batch_op:
batch_op.add_column(sa.Column('cost_centre', sa.String(length=64), nullable=True))
# 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_column('used_cost_centre')
op.create_table('_alembic_tmp__submissionsampleassociation',
sa.Column('sample_id', sa.INTEGER(), nullable=False),
sa.Column('submission_id', sa.INTEGER(), nullable=False),
sa.Column('row', sa.INTEGER(), nullable=False),
sa.Column('column', sa.INTEGER(), nullable=False),
sa.Column('base_sub_type', sa.VARCHAR(), nullable=True),
sa.Column('id', sa.INTEGER(), server_default=sa.text('1'), nullable=False),
sa.ForeignKeyConstraint(['sample_id'], ['_basicsample.id'], ),
sa.ForeignKeyConstraint(['submission_id'], ['_basicsubmission.id'], ),
sa.PrimaryKeyConstraint('submission_id', 'row', 'column'),
sa.UniqueConstraint('id', name='ssa_id')
)
# ### end Alembic commands ###

33
alembic/versions/e6647bd661d9_adding_default_info_to_submissiontype.py Normal file
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@@ -0,0 +1,33 @@
"""adding default info to submissiontype
Revision ID: e6647bd661d9
Revises: f18487b41f45
Create Date: 2024-04-22 12:02:21.512781
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = 'e6647bd661d9'
down_revision = 'f18487b41f45'
branch_labels = None
depends_on = None
def upgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ###
with op.batch_alter_table('_submissiontype', schema=None) as batch_op:
batch_op.add_column(sa.Column('defaults', 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('defaults')
# ### end Alembic commands ###

18
src/submissions/backend/db/models/kits.py
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@@ -374,11 +374,15 @@ class Reagent(BaseClass):
except (TypeError, AttributeError) as e: except (TypeError, AttributeError) as e:
place_holder = date.today() place_holder = date.today()
logger.debug(f"We got a type error setting {self.lot} expiry: {e}. setting to today for testing") logger.debug(f"We got a type error setting {self.lot} expiry: {e}. setting to today for testing")
if self.expiry.year == 1970:
place_holder = "NA"
else:
place_holder = place_holder.strftime("%Y-%m-%d")
return dict( return dict(
name=self.name, name=self.name,
type=rtype, type=rtype,
lot=self.lot, lot=self.lot,
expiry=place_holder.strftime("%Y-%m-%d") expiry=place_holder
) )
def update_last_used(self, kit:KitType) -> Report: def update_last_used(self, kit:KitType) -> Report:
@@ -410,6 +414,7 @@ class Reagent(BaseClass):
@classmethod @classmethod
@setup_lookup @setup_lookup
def query(cls, def query(cls,
id:int|None=None,
reagent_type:str|ReagentType|None=None, reagent_type:str|ReagentType|None=None,
lot_number:str|None=None, lot_number:str|None=None,
name:str|None=None, name:str|None=None,
@@ -428,6 +433,12 @@ class Reagent(BaseClass):
models.Reagent | List[models.Reagent]: reagent or list of reagents matching filter. models.Reagent | List[models.Reagent]: reagent or list of reagents matching filter.
""" """
query: Query = cls.__database_session__.query(cls) query: Query = cls.__database_session__.query(cls)
match id:
case int():
query = query.filter(cls.id==id)
limit = 1
case _:
pass
match reagent_type: match reagent_type:
case str(): case str():
# logger.debug(f"Looking up reagents by reagent type str: {reagent_type}") # logger.debug(f"Looking up reagents by reagent type str: {reagent_type}")
@@ -535,6 +546,7 @@ class SubmissionType(BaseClass):
id = Column(INTEGER, primary_key=True) #: primary key id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(128), unique=True) #: name of submission type name = Column(String(128), unique=True) #: name of submission type
info_map = Column(JSON) #: Where basic information is found in the excel workbook corresponding to this type. info_map = Column(JSON) #: Where basic information is found in the excel workbook corresponding to this type.
defaults = Column(JSON) #: Basic information about this submission type
instances = relationship("BasicSubmission", backref="submission_type") #: Concrete instances of this type. instances = relationship("BasicSubmission", backref="submission_type") #: Concrete instances of this type.
template_file = Column(BLOB) #: Blank form for this type stored as binary. template_file = Column(BLOB) #: Blank form for this type stored as binary.
processes = relationship("Process", back_populates="submission_types", secondary=submissiontypes_processes) #: Relation to equipment processes used for this type. processes = relationship("Process", back_populates="submission_types", secondary=submissiontypes_processes) #: Relation to equipment processes used for this type.
@@ -653,6 +665,10 @@ class SubmissionType(BaseClass):
raise TypeError(f"Type {type(equipment_role)} is not allowed") raise TypeError(f"Type {type(equipment_role)} is not allowed")
return list(set([item for items in relevant for item in items if item != None ])) return list(set([item for items in relevant for item in items if item != None ]))
def get_submission_class(self):
from .submissions import BasicSubmission
return BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.name)
@classmethod @classmethod
@setup_lookup @setup_lookup
def query(cls, def query(cls,

4
src/submissions/backend/db/models/organizations.py
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@@ -65,8 +65,8 @@ class Organization(BaseClass):
pass pass
match name: match name:
case str(): case str():
# logger.debug(f"Looking up organization with name: {name}") # logger.debug(f"Looking up organization with name starting with: {name}")
query = query.filter(cls.name==name) query = query.filter(cls.name.startswith(name))
limit = 1 limit = 1
case _: case _:
pass pass

211
src/submissions/backend/db/models/submissions.py
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@@ -3,12 +3,12 @@ Models for the main submission types.
''' '''
from __future__ import annotations from __future__ import annotations
from getpass import getuser from getpass import getuser
import logging, uuid, tempfile, re, yaml, base64 import logging, uuid, tempfile, re, yaml, base64, sys
from zipfile import ZipFile from zipfile import ZipFile
from tempfile import TemporaryDirectory from tempfile import TemporaryDirectory
from reportlab.graphics.barcode import createBarcodeImageInMemory # from reportlab.graphics.barcode import createBarcodeImageInMemory
from reportlab.graphics.shapes import Drawing # from reportlab.graphics.shapes import Drawing
from reportlab.lib.units import mm # from reportlab.lib.units import mm
from operator import attrgetter, itemgetter from operator import attrgetter, itemgetter
from pprint import pformat from pprint import pformat
from . import BaseClass, Reagent, SubmissionType, KitType, Organization from . import BaseClass, Reagent, SubmissionType, KitType, Organization
@@ -18,9 +18,6 @@ from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLO
from sqlalchemy.orm import relationship, validates, Query from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.orm.attributes import flag_modified from sqlalchemy.orm.attributes import flag_modified
from sqlalchemy.ext.associationproxy import association_proxy from sqlalchemy.ext.associationproxy import association_proxy
# from sqlalchemy.ext.declarative import declared_attr
# from sqlalchemy_json import NestedMutableJson
# from sqlalchemy.ext.mutable import MutableDict
from sqlalchemy.exc import OperationalError as AlcOperationalError, IntegrityError as AlcIntegrityError, StatementError from sqlalchemy.exc import OperationalError as AlcOperationalError, IntegrityError as AlcIntegrityError, StatementError
from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as SQLIntegrityError from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as SQLIntegrityError
import pandas as pd import pandas as pd
@@ -59,9 +56,10 @@ class BasicSubmission(BaseClass):
reagents_id = Column(String, ForeignKey("_reagent.id", ondelete="SET NULL", name="fk_BS_reagents_id")) #: id of used reagents reagents_id = Column(String, ForeignKey("_reagent.id", ondelete="SET NULL", name="fk_BS_reagents_id")) #: id of used reagents
extraction_info = Column(JSON) #: unstructured output from the extraction table logger. extraction_info = Column(JSON) #: unstructured output from the extraction table logger.
run_cost = Column(FLOAT(2)) #: total cost of running the plate. Set from constant and mutable kit costs at time of creation. 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. signed_by = Column(String(32)) #: user name of person who submitted the submission to the database.
comment = Column(JSON) #: user notes comment = Column(JSON) #: user notes
submission_category = Column(String(64)) #: ["Research", "Diagnostic", "Surveillance", "Validation"], else defaults to submission_type_name submission_category = Column(String(64)) #: ["Research", "Diagnostic", "Surveillance", "Validation"], else defaults to submission_type_name
cost_centre = Column(String(64)) #: Permanent storage of used cost centre in case organization field changed in the future.
submission_sample_associations = relationship( submission_sample_associations = relationship(
"SubmissionSampleAssociation", "SubmissionSampleAssociation",
@@ -103,12 +101,59 @@ class BasicSubmission(BaseClass):
return f"{submission_type}Submission({self.rsl_plate_num})" return f"{submission_type}Submission({self.rsl_plate_num})"
@classmethod @classmethod
def jsons(cls): def jsons(cls) -> List[str]:
output = [item.name for item in cls.__table__.columns if isinstance(item.type, JSON)] output = [item.name for item in cls.__table__.columns if isinstance(item.type, JSON)]
if issubclass(cls, BasicSubmission) and not cls.__name__ == "BasicSubmission": if issubclass(cls, BasicSubmission) and not cls.__name__ == "BasicSubmission":
output += BasicSubmission.jsons() output += BasicSubmission.jsons()
return output return output
@classmethod
def get_default_info(cls, *args):
# Create defaults for all submission_types
# print(args)
recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
dicto = dict(
details_ignore = ['excluded', 'reagents', 'samples',
'extraction_info', 'comment', 'barcode',
'platemap', 'export_map', 'equipment'],
form_recover = recover,
form_ignore = ['reagents', 'ctx', 'id', 'cost', 'extraction_info', 'signed_by'] + recover,
parser_ignore = ['samples', 'signed_by'] + cls.jsons(),
excel_ignore = []
)
# Grab subtype specific info.
st = cls.get_submission_type()
if st is None:
logger.error("No default info for BasicSubmission.")
return dicto
else:
dicto['submission_type'] = st.name
output = {}
for k,v in dicto.items():
if len(args) > 0 and k not in args:
logger.debug(f"Don't want {k}")
continue
else:
output[k] = v
for k,v in st.defaults.items():
if len(args) > 0 and k not in args:
logger.debug(f"Don't want {k}")
continue
else:
match v:
case list():
output[k] += v
case _:
output[k] = v
if len(args) == 1:
return output[args[0]]
return output
@classmethod
def get_submission_type(cls):
name = cls.__mapper_args__['polymorphic_identity']
return SubmissionType.query(name=name)
def to_dict(self, full_data:bool=False, backup:bool=False, report:bool=False) -> dict: def to_dict(self, full_data:bool=False, backup:bool=False, report:bool=False) -> dict:
""" """
Constructs dictionary used in submissions summary Constructs dictionary used in submissions summary
@@ -168,6 +213,11 @@ class BasicSubmission(BaseClass):
logger.debug(f"Attempting reagents.") logger.debug(f"Attempting reagents.")
try: try:
reagents = [item.to_sub_dict(extraction_kit=self.extraction_kit) for item in self.submission_reagent_associations] reagents = [item.to_sub_dict(extraction_kit=self.extraction_kit) for item in self.submission_reagent_associations]
for k in self.extraction_kit.construct_xl_map_for_use(self.submission_type):
if k == 'info':
continue
if not any([item['type']==k for item in reagents]):
reagents.append(dict(type=k, name="Not Applicable", lot="NA", expiry=date(year=1970, month=1, day=1), missing=True))
except Exception as e: except Exception as e:
logger.error(f"We got an error retrieving reagents: {e}") logger.error(f"We got an error retrieving reagents: {e}")
reagents = None reagents = None
@@ -181,10 +231,12 @@ class BasicSubmission(BaseClass):
except Exception as e: except Exception as e:
logger.error(f"Error setting equipment: {e}") logger.error(f"Error setting equipment: {e}")
equipment = None equipment = None
cost_centre = self.cost_centre
else: else:
reagents = None reagents = None
samples = None samples = None
equipment = None equipment = None
cost_centre = None
# logger.debug("Getting comments") # logger.debug("Getting comments")
try: try:
comments = self.comment comments = self.comment
@@ -198,6 +250,8 @@ class BasicSubmission(BaseClass):
output["extraction_info"] = ext_info output["extraction_info"] = ext_info
output["comment"] = comments output["comment"] = comments
output["equipment"] = equipment output["equipment"] = equipment
output["Cost Centre"] = cost_centre
output["Signed By"] = self.signed_by
return output return output
def calculate_column_count(self) -> int: def calculate_column_count(self) -> int:
@@ -293,18 +347,18 @@ class BasicSubmission(BaseClass):
""" """
return [item.role for item in self.submission_equipment_associations] return [item.role for item in self.submission_equipment_associations]
def make_plate_barcode(self, width:int=100, height:int=25) -> Drawing: # def make_plate_barcode(self, width:int=100, height:int=25) -> Drawing:
""" # """
Creates a barcode image for this BasicSubmission. # Creates a barcode image for this BasicSubmission.
Args: # Args:
width (int, optional): Width (pixels) of image. Defaults to 100. # width (int, optional): Width (pixels) of image. Defaults to 100.
height (int, optional): Height (pixels) of image. Defaults to 25. # height (int, optional): Height (pixels) of image. Defaults to 25.
Returns: # Returns:
Drawing: image object # Drawing: image object
""" # """
return createBarcodeImageInMemory('Code128', value=self.rsl_plate_num, width=width*mm, height=height*mm, humanReadable=True, format="png") # return createBarcodeImageInMemory('Code128', value=self.rsl_plate_num, width=width*mm, height=height*mm, humanReadable=True, format="png")
@classmethod @classmethod
def submissions_to_df(cls, submission_type:str|None=None, limit:int=0) -> pd.DataFrame: def submissions_to_df(cls, submission_type:str|None=None, limit:int=0) -> pd.DataFrame:
@@ -384,13 +438,19 @@ class BasicSubmission(BaseClass):
case item if item in self.jsons(): case item if item in self.jsons():
logger.debug(f"Setting JSON attribute.") logger.debug(f"Setting JSON attribute.")
existing = self.__getattribute__(key) existing = self.__getattribute__(key)
if value == "" or value is None or value == 'null':
logger.error(f"No value given, not setting.")
return
if existing is None: if existing is None:
existing = [] existing = []
if value in existing: if value in existing:
logger.warning("Value already exists. Preventing duplicate addition.") logger.warning("Value already exists. Preventing duplicate addition.")
return return
else: else:
existing.append(value) if isinstance(value, list):
existing += value
else:
existing.append(value)
self.__setattr__(key, existing) self.__setattr__(key, existing)
flag_modified(self, key) flag_modified(self, key)
return return
@@ -634,7 +694,7 @@ class BasicSubmission(BaseClass):
from backend.validators import RSLNamer from backend.validators import RSLNamer
logger.debug(f"instr coming into {cls}: {instr}") logger.debug(f"instr coming into {cls}: {instr}")
logger.debug(f"data coming into {cls}: {data}") logger.debug(f"data coming into {cls}: {data}")
defaults = cls.get_default_info() defaults = cls.get_default_info("abbreviation", "submission_type")
data['abbreviation'] = defaults['abbreviation'] data['abbreviation'] = defaults['abbreviation']
if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]: if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]:
data['submission_type'] = defaults['submission_type'] data['submission_type'] = defaults['submission_type']
@@ -737,9 +797,7 @@ class BasicSubmission(BaseClass):
Returns: Returns:
Tuple(dict, Template): (Updated dictionary, Template to be rendered) Tuple(dict, Template): (Updated dictionary, Template to be rendered)
""" """
base_dict['excluded'] = ['excluded', 'reagents', 'samples', 'controls', base_dict['excluded'] = cls.get_default_info('details_ignore')
'extraction_info', 'pcr_info', 'comment',
'barcode', 'platemap', 'export_map', 'equipment']
env = jinja_template_loading() env = jinja_template_loading()
temp_name = f"{cls.__name__.lower()}_details.html" temp_name = f"{cls.__name__.lower()}_details.html"
logger.debug(f"Returning template: {temp_name}") logger.debug(f"Returning template: {temp_name}")
@@ -1067,9 +1125,9 @@ class BacterialCulture(BasicSubmission):
output['controls'] = [item.to_sub_dict() for item in self.controls] output['controls'] = [item.to_sub_dict() for item in self.controls]
return output return output
@classmethod # @classmethod
def get_default_info(cls) -> dict: # def get_default_info(cls) -> dict:
return dict(abbreviation="BC", submission_type="Bacterial Culture") # return dict(abbreviation="BC", submission_type="Bacterial Culture")
@classmethod @classmethod
def custom_platemap(cls, xl: pd.ExcelFile, plate_map: pd.DataFrame) -> pd.DataFrame: def custom_platemap(cls, xl: pd.ExcelFile, plate_map: pd.DataFrame) -> pd.DataFrame:
@@ -1214,13 +1272,19 @@ class Wastewater(BasicSubmission):
output['pcr_info'] = self.pcr_info output['pcr_info'] = self.pcr_info
except TypeError as e: except TypeError as e:
pass pass
ext_tech = self.ext_technician or self.technician if self.ext_technician is None or self.ext_technician == "None":
pcr_tech = self.pcr_technician or self.technician output['Ext Technician'] = self.technician
output['Technician'] = f"Enr: {self.technician}, Ext: {ext_tech}, PCR: {pcr_tech}" else:
output["Ext Technician"] = self.ext_technician
if self.pcr_technician is None or self.pcr_technician == "None":
output["PCR Technician"] = self.technician
else:
output['PCR Technician'] = self.pcr_technician
# output['Technician'] = self.technician}, Ext: {ext_tech}, PCR: {pcr_tech}"
return output return output
@classmethod # @classmethod
def get_default_info(cls) -> dict: # def get_default_info(cls) -> dict:
return dict(abbreviation="WW", submission_type="Wastewater") return dict(abbreviation="WW", submission_type="Wastewater")
@classmethod @classmethod
@@ -1334,36 +1398,6 @@ class Wastewater(BasicSubmission):
from frontend.widgets import select_open_file from frontend.widgets import select_open_file
fname = select_open_file(obj=obj, file_extension="xlsx") fname = select_open_file(obj=obj, file_extension="xlsx")
parser = PCRParser(filepath=fname) parser = PCRParser(filepath=fname)
# Check if PCR info already exists
# if hasattr(self, 'pcr_info') and self.pcr_info != None:
# # existing = json.loads(sub.pcr_info)
# existing = self.pcr_info
# logger.debug(f"Found existing pcr info: {pformat(self.pcr_info)}")
# else:
# existing = None
# if existing != None:
# # update pcr_info
# try:
# logger.debug(f"Updating {type(existing)}:\n {pformat(existing)} with {type(parser.pcr)}:\n {pformat(parser.pcr)}")
# # if json.dumps(parser.pcr) not in sub.pcr_info:
# if parser.pcr not in self.pcr_info:
# logger.debug(f"This is new pcr info, appending to existing")
# existing.append(parser.pcr)
# else:
# logger.debug("This info already exists, skipping.")
# # logger.debug(f"Setting {self.rsl_plate_num} PCR to:\n {pformat(existing)}")
# # sub.pcr_info = json.dumps(existing)
# self.pcr_info = existing
# except TypeError:
# logger.error(f"Error updating!")
# # sub.pcr_info = json.dumps([parser.pcr])
# self.pcr_info = [parser.pcr]
# logger.debug(f"Final pcr info for {self.rsl_plate_num}:\n {pformat(self.pcr_info)}")
# else:
# # sub.pcr_info = json.dumps([parser.pcr])
# self.pcr_info = [parser.pcr]
# # logger.debug(f"Existing {type(self.pcr_info)}: {self.pcr_info}")
# # logger.debug(f"Inserting {type(parser.pcr)}: {parser.pcr}")
self.set_attribute("pcr_info", parser.pcr) self.set_attribute("pcr_info", parser.pcr)
self.save(original=False) self.save(original=False)
logger.debug(f"Got {len(parser.samples)} samples to update!") logger.debug(f"Got {len(parser.samples)} samples to update!")
@@ -1390,7 +1424,6 @@ class WastewaterArtic(BasicSubmission):
gel_controls = Column(JSON) #: locations of controls on the gel gel_controls = Column(JSON) #: locations of controls on the gel
source_plates = Column(JSON) #: wastewater plates that samples come from source_plates = Column(JSON) #: wastewater plates that samples come from
__mapper_args__ = dict(polymorphic_identity="Wastewater Artic", __mapper_args__ = dict(polymorphic_identity="Wastewater Artic",
polymorphic_load="inline", polymorphic_load="inline",
inherit_condition=(id == BasicSubmission.id)) inherit_condition=(id == BasicSubmission.id))
@@ -1411,9 +1444,9 @@ class WastewaterArtic(BasicSubmission):
output['source_plates'] = self.source_plates output['source_plates'] = self.source_plates
return output return output
@classmethod # @classmethod
def get_default_info(cls) -> str: # def get_default_info(cls) -> str:
return dict(abbreviation="AR", submission_type="Wastewater Artic") # return dict(abbreviation="AR", submission_type="Wastewater Artic")
@classmethod @classmethod
def parse_info(cls, input_dict:dict, xl:pd.ExcelFile|None=None) -> dict: def parse_info(cls, input_dict:dict, xl:pd.ExcelFile|None=None) -> dict:
@@ -1429,12 +1462,16 @@ class WastewaterArtic(BasicSubmission):
""" """
# from backend.validators import RSLNamer # from backend.validators import RSLNamer
input_dict = super().parse_info(input_dict) input_dict = super().parse_info(input_dict)
ws = load_workbook(xl.io, data_only=True)['Egel results'] workbook = load_workbook(xl.io, data_only=True)
data = [ws.cell(row=jj,column=ii) for ii in range(15,27) for jj in range(10,18)] ws = workbook['Egel results']
data = [ws.cell(row=ii,column=jj) for jj in range(15,27) for ii in range(10,18)]
data = [cell for cell in data if cell.value is not None and "NTC" in cell.value] data = [cell for cell in data if cell.value is not None and "NTC" in cell.value]
input_dict['gel_controls'] = [dict(sample_id=cell.value, location=f"{row_map[cell.row-9]}{str(cell.column-14).zfill(2)}") for cell in data] input_dict['gel_controls'] = [dict(sample_id=cell.value, location=f"{row_map[cell.row-9]}{str(cell.column-14).zfill(2)}") for cell in data]
# df = xl.parse("Egel results").iloc[7:16, 13:26] # df = xl.parse("Egel results").iloc[7:16, 13:26]
# df = df.set_index(df.columns[0]) # df = df.set_index(df.columns[0])
ws = workbook['First Strand List']
data = [dict(plate=ws.cell(row=ii, column=3).value, starting_sample=ws.cell(row=ii, column=4).value) for ii in range(8,11)]
input_dict['source_plates'] = data
return input_dict return input_dict
@classmethod @classmethod
@@ -1500,34 +1537,38 @@ class WastewaterArtic(BasicSubmission):
Returns: Returns:
str: output name str: output name
""" """
logger.debug(f"input string raw: {input_str}")
# Remove letters. # Remove letters.
processed = re.sub(r"[A-Z]", "", input_str) processed = re.sub(r"[A-QS-Z]+\d*", "", input_str)
# Remove trailing '-' if any # Remove trailing '-' if any
processed = processed.strip("-") processed = processed.strip("-")
logger.debug(f"Processed after stripping letters: {processed}")
try: try:
en_num = re.search(r"\-\d{1}$", processed).group() en_num = re.search(r"\-\d{1}$", processed).group()
processed = rreplace(processed, en_num, "") processed = rreplace(processed, en_num, "")
except AttributeError: except AttributeError:
en_num = "1" en_num = "1"
en_num = en_num.strip("-") en_num = en_num.strip("-")
# logger.debug(f"Processed after en-num: {processed}") logger.debug(f"Processed after en-num: {processed}")
try: try:
plate_num = re.search(r"\-\d{1}$", processed).group() plate_num = re.search(r"\-\d{1}R?\d?$", processed).group()
processed = rreplace(processed, plate_num, "") processed = rreplace(processed, plate_num, "")
except AttributeError: except AttributeError:
plate_num = "1" plate_num = "1"
plate_num = plate_num.strip("-") plate_num = plate_num.strip("-")
# logger.debug(f"Processed after plate-num: {processed}") logger.debug(f"Processed after plate-num: {processed}")
day = re.search(r"\d{2}$", processed).group() day = re.search(r"\d{2}$", processed).group()
processed = rreplace(processed, day, "") processed = rreplace(processed, day, "")
# logger.debug(f"Processed after day: {processed}") logger.debug(f"Processed after day: {processed}")
month = re.search(r"\d{2}$", processed).group() month = re.search(r"\d{2}$", processed).group()
processed = rreplace(processed, month, "") processed = rreplace(processed, month, "")
processed = processed.replace("--", "") processed = processed.replace("--", "")
# logger.debug(f"Processed after month: {processed}") logger.debug(f"Processed after month: {processed}")
year = re.search(r'^(?:\d{2})?\d{2}', processed).group() year = re.search(r'^(?:\d{2})?\d{2}', processed).group()
year = f"20{year}" year = f"20{year}"
return f"EN{year}{month}{day}-{en_num}" final_en_name = f"EN{year}{month}{day}-{en_num}"
logger.debug(f"Final EN name: {final_en_name}")
return final_en_name
@classmethod @classmethod
def get_regex(cls) -> str: def get_regex(cls) -> str:
@@ -1599,7 +1640,23 @@ class WastewaterArtic(BasicSubmission):
# for jjj, value in enumerate(plate, start=3): # for jjj, value in enumerate(plate, start=3):
# worksheet.cell(row=iii, column=jjj, value=value) # worksheet.cell(row=iii, column=jjj, value=value)
logger.debug(f"Info:\n{pformat(info)}") logger.debug(f"Info:\n{pformat(info)}")
check = 'gel_info' in info.keys() and info['gel_info']['value'] != None check = 'source_plates' in info.keys() and info['source_plates'] is not None
if check:
worksheet = input_excel['First Strand List']
start_row = 8
for iii, plate in enumerate(info['source_plates']['value']):
logger.debug(f"Plate: {plate}")
row = start_row + iii
try:
worksheet.cell(row=row, column=3, value=plate['plate'])
except TypeError:
pass
try:
worksheet.cell(row=row, column=4, value=plate['starting_sample'])
except TypeError:
pass
# sys.exit(f"Hardcoded stop: backend.models.submissions:1629")
check = 'gel_info' in info.keys() and info['gel_info']['value'] is not None
if check: if check:
# logger.debug(f"Gel info check passed.") # logger.debug(f"Gel info check passed.")
if info['gel_info'] != None: if info['gel_info'] != None:
@@ -1618,7 +1675,7 @@ class WastewaterArtic(BasicSubmission):
column = start_column + 2 + jjj column = start_column + 2 + jjj
worksheet.cell(row=start_row, column=column, value=kj['name']) worksheet.cell(row=start_row, column=column, value=kj['name'])
worksheet.cell(row=row, column=column, value=kj['value']) worksheet.cell(row=row, column=column, value=kj['value'])
check = 'gel_image' in info.keys() and info['gel_image']['value'] != None check = 'gel_image' in info.keys() and info['gel_image']['value'] is not None
if check: if check:
if info['gel_image'] != None: if info['gel_image'] != None:
worksheet = input_excel['Egel results'] worksheet = input_excel['Egel results']

43
src/submissions/backend/excel/parser.py
View File

@@ -62,9 +62,11 @@ class SheetParser(object):
parser = InfoParser(xl=self.xl, submission_type=self.sub['submission_type']['value']) parser = InfoParser(xl=self.xl, submission_type=self.sub['submission_type']['value'])
info = parser.parse_info() info = parser.parse_info()
self.info_map = parser.map self.info_map = parser.map
# exclude_from_info = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.sub['submission_type']).exclude_from_info_parser()
for k,v in info.items(): for k,v in info.items():
match k: match k:
case "sample": case "sample":
# case item if
pass pass
case _: case _:
self.sub[k] = v self.sub[k] = v
@@ -97,9 +99,9 @@ class SheetParser(object):
""" """
Enforce that the parser has an extraction kit Enforce that the parser has an extraction kit
""" """
from frontend.widgets.pop_ups import KitSelector from frontend.widgets.pop_ups import ObjectSelector
if not check_not_nan(self.sub['extraction_kit']['value']): if not check_not_nan(self.sub['extraction_kit']['value']):
dlg = KitSelector(title="Kit Needed", message="At minimum a kit is needed. Please select one.") dlg = ObjectSelector(title="Kit Needed", message="At minimum a kit is needed. Please select one.", obj_type=KitType)
if dlg.exec(): if dlg.exec():
self.sub['extraction_kit'] = dict(value=dlg.getValues(), missing=True) self.sub['extraction_kit'] = dict(value=dlg.getValues(), missing=True)
else: else:
@@ -133,7 +135,11 @@ class SheetParser(object):
""" """
# logger.debug(f"Submission dictionary coming into 'to_pydantic':\n{pformat(self.sub)}") # logger.debug(f"Submission dictionary coming into 'to_pydantic':\n{pformat(self.sub)}")
logger.debug(f"Equipment: {self.sub['equipment']}") logger.debug(f"Equipment: {self.sub['equipment']}")
if len(self.sub['equipment']) == 0: try:
check = len(self.sub['equipment']) == 0
except TypeError:
check = True
if check:
self.sub['equipment'] = None self.sub['equipment'] = None
psm = PydSubmission(filepath=self.filepath, **self.sub) psm = PydSubmission(filepath=self.filepath, **self.sub)
return psm return psm
@@ -142,11 +148,12 @@ class InfoParser(object):
def __init__(self, xl:pd.ExcelFile, submission_type:str): def __init__(self, xl:pd.ExcelFile, submission_type:str):
logger.info(f"\n\Hello from InfoParser!\n\n") logger.info(f"\n\Hello from InfoParser!\n\n")
self.map = self.fetch_submission_info_map(submission_type=submission_type) self.submission_type = submission_type
self.map = self.fetch_submission_info_map()
self.xl = xl self.xl = xl
logger.debug(f"Info map for InfoParser: {pformat(self.map)}") logger.debug(f"Info map for InfoParser: {pformat(self.map)}")
def fetch_submission_info_map(self, submission_type:str|dict) -> dict: def fetch_submission_info_map(self) -> dict:
""" """
Gets location of basic info from the submission_type object in the database. Gets location of basic info from the submission_type object in the database.
@@ -156,10 +163,10 @@ class InfoParser(object):
Returns: Returns:
dict: Location map of all info for this submission type dict: Location map of all info for this submission type
""" """
if isinstance(submission_type, str): if isinstance(self.submission_type, str):
submission_type = dict(value=submission_type, missing=True) self.submission_type = dict(value=self.submission_type, missing=True)
logger.debug(f"Looking up submission type: {submission_type['value']}") logger.debug(f"Looking up submission type: {self.submission_type['value']}")
submission_type = SubmissionType.query(name=submission_type['value']) submission_type = SubmissionType.query(name=self.submission_type['value'])
info_map = submission_type.info_map info_map = submission_type.info_map
# Get the parse_info method from the submission type specified # Get the parse_info method from the submission type specified
self.custom_parser = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=submission_type.name).parse_info self.custom_parser = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=submission_type.name).parse_info
@@ -172,16 +179,25 @@ class InfoParser(object):
Returns: Returns:
dict: key:value of basic info dict: key:value of basic info
""" """
if isinstance(self.submission_type, str):
self.submission_type = dict(value=self.submission_type, missing=True)
dicto = {} dicto = {}
exclude_from_generic = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type['value']).get_default_info("parser_ignore")
# This loop parses generic info
logger.debug(f"Map: {self.map}")
# time.sleep(5)
for sheet in self.xl.sheet_names: for sheet in self.xl.sheet_names:
df = self.xl.parse(sheet, header=None) df = self.xl.parse(sheet, header=None)
relevant = {} relevant = {}
for k, v in self.map.items(): for k, v in self.map.items():
# exclude from generic parsing
if k in exclude_from_generic:
continue
# If the value is hardcoded put it in the dictionary directly.
if isinstance(v, str): if isinstance(v, str):
dicto[k] = dict(value=v, missing=False) dicto[k] = dict(value=v, missing=False)
continue continue
if k in ["samples", "all_sheets"]: logger.debug(f"Looking for {k} in self.map")
continue
if sheet in self.map[k]['sheets']: if sheet in self.map[k]['sheets']:
relevant[k] = v relevant[k] = v
logger.debug(f"relevant map for {sheet}: {pformat(relevant)}") logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
@@ -252,6 +268,7 @@ class ReagentParser(object):
lot = df.iat[relevant[item]['lot']['row']-1, relevant[item]['lot']['column']-1] lot = df.iat[relevant[item]['lot']['row']-1, relevant[item]['lot']['column']-1]
expiry = df.iat[relevant[item]['expiry']['row']-1, relevant[item]['expiry']['column']-1] expiry = df.iat[relevant[item]['expiry']['row']-1, relevant[item]['expiry']['column']-1]
if 'comment' in relevant[item].keys(): if 'comment' in relevant[item].keys():
logger.debug(f"looking for {relevant[item]} comment.")
comment = df.iat[relevant[item]['comment']['row']-1, relevant[item]['comment']['column']-1] comment = df.iat[relevant[item]['comment']['row']-1, relevant[item]['comment']['column']-1]
else: else:
comment = "" comment = ""
@@ -294,7 +311,7 @@ class SampleParser(object):
sample_info_map = self.fetch_sample_info_map(submission_type=submission_type, sample_map=sample_map) sample_info_map = self.fetch_sample_info_map(submission_type=submission_type, sample_map=sample_map)
logger.debug(f"sample_info_map: {sample_info_map}") logger.debug(f"sample_info_map: {sample_info_map}")
self.plate_map = self.construct_plate_map(plate_map_location=sample_info_map['plate_map']) self.plate_map = self.construct_plate_map(plate_map_location=sample_info_map['plate_map'])
logger.debug(f"plate_map: {self.plate_map}") # logger.debug(f"plate_map: {self.plate_map}")
self.lookup_table = self.construct_lookup_table(lookup_table_location=sample_info_map['lookup_table']) self.lookup_table = self.construct_lookup_table(lookup_table_location=sample_info_map['lookup_table'])
if "plates" in sample_info_map: if "plates" in sample_info_map:
self.plates = sample_info_map['plates'] self.plates = sample_info_map['plates']
@@ -439,7 +456,7 @@ class SampleParser(object):
""" """
result = None result = None
new_samples = [] new_samples = []
logger.debug(f"Starting samples: {pformat(self.samples)}") # logger.debug(f"Starting samples: {pformat(self.samples)}")
for sample in self.samples: for sample in self.samples:
translated_dict = {} translated_dict = {}
for k, v in sample.items(): for k, v in sample.items():

4
src/submissions/backend/validators/__init__.py
View File

@@ -74,8 +74,8 @@ class RSLNamer(object):
check = True check = True
if check: if check:
# logger.debug("Final option, ask the user for submission type") # logger.debug("Final option, ask the user for submission type")
from frontend.widgets import SubmissionTypeSelector from frontend.widgets import ObjectSelector
dlg = SubmissionTypeSelector(title="Couldn't parse submission type.", message="Please select submission type from list below.") dlg = ObjectSelector(title="Couldn't parse submission type.", message="Please select submission type from list below.", obj_type=SubmissionType)
if dlg.exec(): if dlg.exec():
submission_type = dlg.parse_form() submission_type = dlg.parse_form()
submission_type = submission_type.replace("_", " ") submission_type = submission_type.replace("_", " ")

115
src/submissions/backend/validators/pydant.py
View File

@@ -8,13 +8,13 @@ from pydantic import BaseModel, field_validator, Field
from datetime import date, datetime, timedelta from datetime import date, datetime, timedelta
from dateutil.parser import parse from dateutil.parser import parse
from dateutil.parser._parser import ParserError from dateutil.parser._parser import ParserError
from typing import List, Tuple from typing import List, Tuple, Literal
from . import RSLNamer from . import RSLNamer
from pathlib import Path from pathlib import Path
from tools import check_not_nan, convert_nans_to_nones, Report, Result, row_map from tools import check_not_nan, convert_nans_to_nones, Report, Result, row_map
from backend.db.models import * from backend.db.models import *
from sqlalchemy.exc import StatementError, IntegrityError from sqlalchemy.exc import StatementError, IntegrityError
from PyQt6.QtWidgets import QComboBox, QWidget from PyQt6.QtWidgets import QWidget
from openpyxl import load_workbook, Workbook from openpyxl import load_workbook, Workbook
from io import BytesIO from io import BytesIO
@@ -24,7 +24,7 @@ class PydReagent(BaseModel):
lot: str|None lot: str|None
type: str|None type: str|None
expiry: date|None expiry: date|Literal['NA']|None
name: str|None name: str|None
missing: bool = Field(default=True) missing: bool = Field(default=True)
comment: str|None = Field(default="", validate_default=True) comment: str|None = Field(default="", validate_default=True)
@@ -77,6 +77,8 @@ class PydReagent(BaseModel):
match value: match value:
case int(): case int():
return datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value - 2).date() return datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value - 2).date()
case 'NA':
return value
case str(): case str():
return parse(value) return parse(value)
case date(): case date():
@@ -87,6 +89,13 @@ class PydReagent(BaseModel):
value = date.today() value = date.today()
return value return value
@field_validator("expiry")
@classmethod
def date_na(cls, value):
if isinstance(value, date) and value.year == 1970:
value = "NA"
return value
@field_validator("name", mode="before") @field_validator("name", mode="before")
@classmethod @classmethod
def enforce_name(cls, value, values): def enforce_name(cls, value, values):
@@ -125,6 +134,10 @@ class PydReagent(BaseModel):
reagent.type.append(reagent_type) reagent.type.append(reagent_type)
case "comment": case "comment":
continue continue
case "expiry":
if isinstance(value, str):
value = date(year=1970, month=1, day=1)
reagent.expiry = value
case _: case _:
try: try:
reagent.__setattr__(key, value) reagent.__setattr__(key, value)
@@ -271,6 +284,7 @@ class PydSubmission(BaseModel, extra='allow'):
reagents: List[dict]|List[PydReagent] = [] reagents: List[dict]|List[PydReagent] = []
samples: List[PydSample] samples: List[PydSample]
equipment: List[PydEquipment]|None =[] equipment: List[PydEquipment]|None =[]
cost_centre: dict|None = Field(default=dict(value=None, missing=True), validate_default=True)
@field_validator('equipment', mode='before') @field_validator('equipment', mode='before')
@classmethod @classmethod
@@ -332,10 +346,28 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("submitting_lab", mode="before") @field_validator("submitting_lab", mode="before")
@classmethod @classmethod
def rescue_submitting_lab(cls, value): def rescue_submitting_lab(cls, value):
if value == None: if value is None:
return dict(value=None, missing=True) return dict(value=None, missing=True)
return value return value
@field_validator("submitting_lab")
@classmethod
def lookup_submitting_lab(cls, value):
if isinstance(value['value'], str):
try:
value['value'] = Organization.query(name=value['value']).name
except AttributeError:
value['value'] = None
if value['value'] is None:
value['missing'] = True
from frontend.widgets.pop_ups import ObjectSelector
dlg = ObjectSelector(title="Missing Submitting Lab", message="We need a submitting lab. Please select from the list.", obj_type=Organization)
if dlg.exec():
value['value'] = dlg.getValues()
else:
value['value'] = None
return value
@field_validator("rsl_plate_num", mode='before') @field_validator("rsl_plate_num", mode='before')
@classmethod @classmethod
def rescue_rsl_number(cls, value): def rescue_rsl_number(cls, value):
@@ -427,6 +459,30 @@ class PydSubmission(BaseModel, extra='allow'):
output.append(sample) output.append(sample)
return output return output
@field_validator("cost_centre", mode="before")
@classmethod
def rescue_cost_centre(cls, value):
match value:
case dict():
return value
case _:
return dict(value=value, missing=True)
@field_validator("cost_centre")
@classmethod
def get_cost_centre(cls, value, values):
# logger.debug(f"Value coming in for cost_centre: {value}")
match value['value']:
case None:
from backend.db.models import Organization
org = Organization.query(name=values.data['submitting_lab']['value'])
try:
return dict(value=org.cost_centre, missing=True)
except AttributeError:
return dict(value="xxx", missing=True)
case _:
return value
def set_attribute(self, key, value): def set_attribute(self, key, value):
self.__setattr__(name=key, value=value) self.__setattr__(name=key, value=value)
@@ -599,6 +655,7 @@ class PydSubmission(BaseModel, extra='allow'):
else: else:
info = {k:v for k,v in self.improved_dict().items() if isinstance(v, dict)} info = {k:v for k,v in self.improved_dict().items() if isinstance(v, dict)}
reagents = self.reagents reagents = self.reagents
if len(reagents + list(info.keys())) == 0: if len(reagents + list(info.keys())) == 0:
# logger.warning("No info to fill in, returning") # logger.warning("No info to fill in, returning")
return None return None
@@ -616,14 +673,14 @@ class PydSubmission(BaseModel, extra='allow'):
new_reagent = {} new_reagent = {}
new_reagent['type'] = reagent.type new_reagent['type'] = reagent.type
new_reagent['lot'] = excel_map[new_reagent['type']]['lot'] new_reagent['lot'] = excel_map[new_reagent['type']]['lot']
new_reagent['lot']['value'] = reagent.lot new_reagent['lot']['value'] = reagent.lot or "NA"
new_reagent['expiry'] = excel_map[new_reagent['type']]['expiry'] new_reagent['expiry'] = excel_map[new_reagent['type']]['expiry']
new_reagent['expiry']['value'] = reagent.expiry new_reagent['expiry']['value'] = reagent.expiry or "NA"
new_reagent['sheet'] = excel_map[new_reagent['type']]['sheet'] new_reagent['sheet'] = excel_map[new_reagent['type']]['sheet']
# name is only present for Bacterial Culture # name is only present for Bacterial Culture
try: try:
new_reagent['name'] = excel_map[new_reagent['type']]['name'] new_reagent['name'] = excel_map[new_reagent['type']]['name']
new_reagent['name']['value'] = reagent.name new_reagent['name']['value'] = reagent.name or "Not Applicable"
except Exception as e: except Exception as e:
logger.error(f"Couldn't get name due to {e}") logger.error(f"Couldn't get name due to {e}")
new_reagents.append(new_reagent) new_reagents.append(new_reagent)
@@ -657,6 +714,8 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug(f"Attempting to write lot {reagent['lot']['value']} in: row {reagent['lot']['row']}, column {reagent['lot']['column']}") # logger.debug(f"Attempting to write lot {reagent['lot']['value']} in: row {reagent['lot']['row']}, column {reagent['lot']['column']}")
worksheet.cell(row=reagent['lot']['row'], column=reagent['lot']['column'], value=reagent['lot']['value']) worksheet.cell(row=reagent['lot']['row'], column=reagent['lot']['column'], value=reagent['lot']['value'])
# logger.debug(f"Attempting to write expiry {reagent['expiry']['value']} in: row {reagent['expiry']['row']}, column {reagent['expiry']['column']}") # logger.debug(f"Attempting to write expiry {reagent['expiry']['value']} in: row {reagent['expiry']['row']}, column {reagent['expiry']['column']}")
if reagent['expiry']['value'].year == 1970:
reagent['expiry']['value'] = "NA"
worksheet.cell(row=reagent['expiry']['row'], column=reagent['expiry']['column'], value=reagent['expiry']['value']) worksheet.cell(row=reagent['expiry']['row'], column=reagent['expiry']['column'], value=reagent['expiry']['value'])
try: try:
# logger.debug(f"Attempting to write name {reagent['name']['value']} in: row {reagent['name']['row']}, column {reagent['name']['column']}") # logger.debug(f"Attempting to write name {reagent['name']['value']} in: row {reagent['name']['row']}, column {reagent['name']['column']}")
@@ -790,14 +849,13 @@ class PydSubmission(BaseModel, extra='allow'):
logger.debug(f"Extraction kit: {extraction_kit}. Is it a string? {isinstance(extraction_kit, str)}") logger.debug(f"Extraction kit: {extraction_kit}. Is it a string? {isinstance(extraction_kit, str)}")
if isinstance(extraction_kit, str): if isinstance(extraction_kit, str):
extraction_kit = dict(value=extraction_kit) extraction_kit = dict(value=extraction_kit)
if extraction_kit is not None: if extraction_kit is not None and extraction_kit != self.extraction_kit['value']:
if extraction_kit != self.extraction_kit['value']:
self.extraction_kit['value'] = extraction_kit['value'] self.extraction_kit['value'] = extraction_kit['value']
reagenttypes = [] # reagenttypes = []
else: # else:
reagenttypes = [item.type for item in self.reagents] # reagenttypes = [item.type for item in self.reagents]
else: # else:
reagenttypes = [item.type for item in self.reagents] # reagenttypes = [item.type for item in self.reagents]
logger.debug(f"Looking up {self.extraction_kit['value']}") logger.debug(f"Looking up {self.extraction_kit['value']}")
ext_kit = KitType.query(name=self.extraction_kit['value']) ext_kit = KitType.query(name=self.extraction_kit['value'])
ext_kit_rtypes = [item.to_pydantic() for item in ext_kit.get_reagents(required=True, submission_type=self.submission_type['value'])] ext_kit_rtypes = [item.to_pydantic() for item in ext_kit.get_reagents(required=True, submission_type=self.submission_type['value'])]
@@ -808,21 +866,26 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug(f"Checking if reagents match kit contents: {check}") # logger.debug(f"Checking if reagents match kit contents: {check}")
# # what reagent types are in both lists? # # what reagent types are in both lists?
# missing = list(set(ext_kit_rtypes).difference(reagenttypes)) # missing = list(set(ext_kit_rtypes).difference(reagenttypes))
missing = [] # missing = []
output_reagents = self.reagents # Exclude any reagenttype found in this pyd not expected in kit.
# output_reagents = ext_kit_rtypes expected_check = [item.type for item in ext_kit_rtypes]
logger.debug(f"Already have these reagent types: {reagenttypes}") output_reagents = [rt for rt in self.reagents if rt.type in expected_check]
for rt in ext_kit_rtypes: logger.debug(f"Already have these reagent types: {output_reagents}")
if rt.type not in reagenttypes: missing_check = [item.type for item in output_reagents]
missing.append(rt) missing_reagents = [rt for rt in ext_kit_rtypes if rt.type not in missing_check]
if rt.type not in [item.type for item in output_reagents]: missing_reagents += [rt for rt in output_reagents if rt.missing]
output_reagents.append(rt) # for rt in ext_kit_rtypes:
logger.debug(f"Missing reagents types: {missing}") # if rt.type not in [item.type for item in output_reagents]:
# missing.append(rt)
# if rt.type not in [item.type for item in output_reagents]:
# output_reagents.append(rt)
output_reagents += [rt for rt in missing_reagents if rt not in output_reagents]
logger.debug(f"Missing reagents types: {missing_reagents}")
# if lists are equal return no problem # if lists are equal return no problem
if len(missing)==0: if len(missing_reagents)==0:
result = None result = None
else: else:
result = Result(msg=f"The submission you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.type.upper() for item in missing]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!", status="Warning") result = Result(msg=f"The excel sheet you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.type.upper() for item in missing_reagents]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!", status="Warning")
report.add_result(result) report.add_result(result)
return output_reagents, report return output_reagents, report

6
src/submissions/frontend/widgets/misc.py
View File

@@ -85,10 +85,10 @@ class AddReagentForm(QDialog):
Returns: Returns:
dict: Output info dict: Output info
""" """
return dict(name=self.name_input.currentText(), return dict(name=self.name_input.currentText().strip(),
lot=self.lot_input.text(), lot=self.lot_input.text().strip(),
expiry=self.exp_input.date().toPyDate(), expiry=self.exp_input.date().toPyDate(),
type=self.type_input.currentText()) type=self.type_input.currentText().strip())
def update_names(self): def update_names(self):
""" """

109
src/submissions/frontend/widgets/pop_ups.py
View File

@@ -7,7 +7,7 @@ from PyQt6.QtWidgets import (
) )
from tools import jinja_template_loading from tools import jinja_template_loading
import logging import logging
from backend.db.models import KitType, SubmissionType from backend.db import models
from typing import Literal from typing import Literal
logger = logging.getLogger(f"submissions.{__name__}") logger = logging.getLogger(f"submissions.{__name__}")
@@ -45,16 +45,18 @@ class AlertPop(QMessageBox):
self.setInformativeText(message) self.setInformativeText(message)
self.setWindowTitle(f"{owner} - {status.title()}") self.setWindowTitle(f"{owner} - {status.title()}")
class KitSelector(QDialog): class ObjectSelector(QDialog):
""" """
dialog to input KitType manually dialog to input BaseClass type manually
""" """
def __init__(self, title:str, message:str) -> QDialog: def __init__(self, title:str, message:str, obj_type:str|models.BaseClass) -> QDialog:
super().__init__() super().__init__()
self.setWindowTitle(title) self.setWindowTitle(title)
self.widget = QComboBox() self.widget = QComboBox()
kits = [item.name for item in KitType.query()] if isinstance(obj_type, str):
self.widget.addItems(kits) obj_type: models.BaseClass = getattr(models, obj_type)
items = [item.name for item in obj_type.query()]
self.widget.addItems(items)
self.widget.setEditable(False) self.widget.setEditable(False)
# set yes/no buttons # set yes/no buttons
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
@@ -78,36 +80,69 @@ class KitSelector(QDialog):
""" """
return self.widget.currentText() return self.widget.currentText()
class SubmissionTypeSelector(QDialog): # class KitSelector(QDialog):
""" # """
dialog to input SubmissionType manually # dialog to input KitType manually
""" # """
def __init__(self, title:str, message:str) -> QDialog: # def __init__(self, title:str, message:str) -> QDialog:
super().__init__() # super().__init__()
self.setWindowTitle(title) # self.setWindowTitle(title)
self.widget = QComboBox() # self.widget = QComboBox()
# sub_type = [item.name for item in lookup_submission_type(ctx=ctx)] # kits = [item.name for item in KitType.query()]
sub_type = [item.name for item in SubmissionType.query()] # self.widget.addItems(kits)
self.widget.addItems(sub_type) # self.widget.setEditable(False)
self.widget.setEditable(False) # # set yes/no buttons
# set yes/no buttons # QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel # self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox = QDialogButtonBox(QBtn) # self.buttonBox.accepted.connect(self.accept)
self.buttonBox.accepted.connect(self.accept) # self.buttonBox.rejected.connect(self.reject)
self.buttonBox.rejected.connect(self.reject) # self.layout = QVBoxLayout()
self.layout = QVBoxLayout() # # Text for the yes/no question
# Text for the yes/no question # message = QLabel(message)
message = QLabel(message) # self.layout.addWidget(message)
self.layout.addWidget(message) # self.layout.addWidget(self.widget)
self.layout.addWidget(self.widget) # self.layout.addWidget(self.buttonBox)
self.layout.addWidget(self.buttonBox) # self.setLayout(self.layout)
self.setLayout(self.layout)
def parse_form(self) -> str: # def getValues(self) -> str:
""" # """
Pulls SubmissionType(str) from widget # Get KitType(str) from widget
Returns: # Returns:
str: SubmissionType as str # str: KitType as str
""" # """
return self.widget.currentText() # return self.widget.currentText()
# class SubmissionTypeSelector(QDialog):
# """
# dialog to input SubmissionType manually
# """
# def __init__(self, title:str, message:str) -> QDialog:
# super().__init__()
# self.setWindowTitle(title)
# self.widget = QComboBox()
# # sub_type = [item.name for item in lookup_submission_type(ctx=ctx)]
# sub_type = [item.name for item in SubmissionType.query()]
# self.widget.addItems(sub_type)
# self.widget.setEditable(False)
# # set yes/no buttons
# QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
# self.buttonBox = QDialogButtonBox(QBtn)
# self.buttonBox.accepted.connect(self.accept)
# self.buttonBox.rejected.connect(self.reject)
# self.layout = QVBoxLayout()
# # Text for the yes/no question
# message = QLabel(message)
# self.layout.addWidget(message)
# self.layout.addWidget(self.widget)
# self.layout.addWidget(self.buttonBox)
# self.setLayout(self.layout)
# def parse_form(self) -> str:
# """
# Pulls SubmissionType(str) from widget
# Returns:
# str: SubmissionType as str
# """
# return self.widget.currentText()

21
src/submissions/frontend/widgets/submission_details.py
View File

@@ -5,12 +5,12 @@ from PyQt6.QtWebChannel import QWebChannel
from PyQt6.QtCore import Qt, pyqtSlot from PyQt6.QtCore import Qt, pyqtSlot
from backend.db.models import BasicSubmission, BasicSample from backend.db.models import BasicSubmission, BasicSample
from tools import check_if_app, check_authorization, is_power_user from tools import is_power_user, html_to_pdf
from .functions import select_save_file from .functions import select_save_file
from io import BytesIO from io import BytesIO
from tempfile import TemporaryFile, TemporaryDirectory from tempfile import TemporaryFile, TemporaryDirectory
from pathlib import Path from pathlib import Path
from xhtml2pdf import pisa # from xhtml2pdf import pisa
import logging, base64 import logging, base64
from getpass import getuser from getpass import getuser
from datetime import datetime from datetime import datetime
@@ -54,6 +54,7 @@ class SubmissionDetails(QDialog):
self.channel = QWebChannel() self.channel = QWebChannel()
self.channel.registerObject('backend', self) self.channel.registerObject('backend', self)
self.submission_details(submission=sub) self.submission_details(submission=sub)
self.rsl_plate_num = sub.rsl_plate_num
self.webview.page().setWebChannel(self.channel) self.webview.page().setWebChannel(self.channel)
@pyqtSlot(str) @pyqtSlot(str)
@@ -86,9 +87,9 @@ class SubmissionDetails(QDialog):
logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k != 'samples'})}") logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k != 'samples'})}")
# don't want id # don't want id
del self.base_dict['id'] del self.base_dict['id']
logger.debug(f"Creating barcode.") # logger.debug(f"Creating barcode.")
if not check_if_app(): # if not check_if_app():
self.base_dict['barcode'] = base64.b64encode(submission.make_plate_barcode(width=120, height=30)).decode('utf-8') # self.base_dict['barcode'] = base64.b64encode(submission.make_plate_barcode(width=120, height=30)).decode('utf-8')
logger.debug(f"Making platemap...") logger.debug(f"Making platemap...")
self.base_dict['platemap'] = submission.make_plate_map() self.base_dict['platemap'] = submission.make_plate_map()
self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict) self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict)
@@ -103,8 +104,9 @@ class SubmissionDetails(QDialog):
logger.debug(f"Signing off on {submission} - ({getuser()})") logger.debug(f"Signing off on {submission} - ({getuser()})")
if isinstance(submission, str): if isinstance(submission, str):
submission = BasicSubmission.query(rsl_number=submission) submission = BasicSubmission.query(rsl_number=submission)
submission.uploaded_by = getuser() submission.signed_by = getuser()
submission.save() submission.save()
self.submission_details(submission=self.rsl_plate_num)
def export(self): def export(self):
""" """
@@ -113,7 +115,7 @@ class SubmissionDetails(QDialog):
fname = select_save_file(obj=self, default_name=self.base_dict['Plate Number'], extension="pdf") fname = select_save_file(obj=self, default_name=self.base_dict['Plate Number'], extension="pdf")
image_io = BytesIO() image_io = BytesIO()
temp_dir = Path(TemporaryDirectory().name) temp_dir = Path(TemporaryDirectory().name)
hti = Html2Image(output_path=temp_dir, size=(1200, 750)) hti = Html2Image(output_path=temp_dir, size=(2400, 1500))
temp_file = Path(TemporaryFile(dir=temp_dir, suffix=".png").name) temp_file = Path(TemporaryFile(dir=temp_dir, suffix=".png").name)
screenshot = hti.screenshot(self.base_dict['platemap'], save_as=temp_file.name) screenshot = hti.screenshot(self.base_dict['platemap'], save_as=temp_file.name)
export_map = Image.open(screenshot[0]) export_map = Image.open(screenshot[0])
@@ -126,8 +128,9 @@ class SubmissionDetails(QDialog):
del self.base_dict['platemap'] del self.base_dict['platemap']
self.html2 = self.template.render(sub=self.base_dict) self.html2 = self.template.render(sub=self.base_dict)
try: try:
with open(fname, "w+b") as f: # with open(fname, "w+b") as f:
pisa.CreatePDF(self.html2, dest=f) # pisa.CreatePDF(self.html2, dest=f)
html_to_pdf(html=self.html2, output_file=fname)
except PermissionError as e: except PermissionError as e:
logger.error(f"Error saving pdf: {e}") logger.error(f"Error saving pdf: {e}")
msg = QMessageBox() msg = QMessageBox()

9
src/submissions/frontend/widgets/submission_table.py
View File

@@ -8,8 +8,8 @@ from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
from PyQt6.QtGui import QAction, QCursor from PyQt6.QtGui import QAction, QCursor
from backend.db.models import BasicSubmission from backend.db.models import BasicSubmission
from backend.excel import make_report_html, make_report_xlsx from backend.excel import make_report_html, make_report_xlsx
from tools import Report, Result, row_map, get_first_blank_df_row from tools import Report, Result, row_map, get_first_blank_df_row, html_to_pdf
from xhtml2pdf import pisa # from xhtml2pdf import pisa
from .functions import select_save_file, select_open_file from .functions import select_save_file, select_open_file
from .misc import ReportDatePicker from .misc import ReportDatePicker
import pandas as pd import pandas as pd
@@ -324,8 +324,9 @@ class SubmissionsSheet(QTableView):
html = make_report_html(df=summary_df, start_date=info['start_date'], end_date=info['end_date']) html = make_report_html(df=summary_df, start_date=info['start_date'], end_date=info['end_date'])
# get save location of report # get save location of report
fname = select_save_file(obj=self, default_name=f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf", extension="pdf") fname = select_save_file(obj=self, default_name=f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf", extension="pdf")
with open(fname, "w+b") as f: # with open(fname, "w+b") as f:
pisa.CreatePDF(html, dest=f) # pisa.CreatePDF(html, dest=f)
html_to_pdf(html=html, output_file=fname)
writer = pd.ExcelWriter(fname.with_suffix(".xlsx"), engine='openpyxl') writer = pd.ExcelWriter(fname.with_suffix(".xlsx"), engine='openpyxl')
summary_df.to_excel(writer, sheet_name="Report") summary_df.to_excel(writer, sheet_name="Report")
detailed_df.to_excel(writer, sheet_name="Details", index=False) detailed_df.to_excel(writer, sheet_name="Details", index=False)

78
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -135,7 +135,7 @@ class SubmissionFormContainer(QWidget):
info = dlg.parse_form() info = dlg.parse_form()
logger.debug(f"Reagent info: {info}") logger.debug(f"Reagent info: {info}")
# create reagent object # create reagent object
reagent = PydReagent(ctx=self.app.ctx, **info) reagent = PydReagent(ctx=self.app.ctx, **info, missing=False)
# send reagent to db # send reagent to db
sqlobj, result = reagent.toSQL() sqlobj, result = reagent.toSQL()
sqlobj.save() sqlobj.save()
@@ -150,45 +150,29 @@ class SubmissionFormWidget(QWidget):
# self.report = Report() # self.report = Report()
self.app = parent.app self.app = parent.app
self.pyd = submission self.pyd = submission
# self.input = [{k:v} for k,v in kwargs.items()]
# self.samples = []
self.missing_info = [] self.missing_info = []
self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx', 'comment', st = SubmissionType.query(name=self.pyd.submission_type['value']).get_submission_class()
'equipment', 'gel_controls', 'id', 'cost', 'extraction_info', defaults = st.get_default_info("form_recover", "form_ignore")
'controls', 'pcr_info', 'gel_info', 'gel_image'] self.recover = defaults['form_recover']
self.recover = ['filepath', 'samples', 'csv', 'comment', 'equipment'] self.ignore = defaults['form_ignore']
# self.ignore += self.recover
# logger.debug(f"Attempting to extend ignore list with {self.pyd.submission_type['value']}")
self.layout = QVBoxLayout() self.layout = QVBoxLayout()
# for k, v in kwargs.items(): # for k, v in kwargs.items():
for k in list(self.pyd.model_fields.keys()) + list(self.pyd.model_extra.keys()): for k in list(self.pyd.model_fields.keys()) + list(self.pyd.model_extra.keys()):
if k not in self.ignore: if k in self.ignore:
try: continue
value = self.pyd.__getattribute__(k) try:
except AttributeError: value = self.pyd.__getattribute__(k)
logger.error(f"Couldn't get attribute from pyd: {k}") except AttributeError:
value = dict(value=None, missing=True) logger.error(f"Couldn't get attribute from pyd: {k}")
add_widget = self.create_widget(key=k, value=value, submission_type=self.pyd.submission_type['value']) value = dict(value=None, missing=True)
if add_widget != None: add_widget = self.create_widget(key=k, value=value, submission_type=self.pyd.submission_type['value'])
self.layout.addWidget(add_widget) if add_widget != None:
if k == "extraction_kit": self.layout.addWidget(add_widget)
add_widget.input.currentTextChanged.connect(self.scrape_reagents) if k == "extraction_kit":
# else: add_widget.input.currentTextChanged.connect(self.scrape_reagents)
# self.__setattr__(k, v)
# self.scrape_reagents(self.extraction_kit['value'])
self.scrape_reagents(self.pyd.extraction_kit) self.scrape_reagents(self.pyd.extraction_kit)
# extraction kit must be added last so widget order makes sense.
# self.layout.addWidget(self.create_widget(key="extraction_kit", value=self.extraction_kit, submission_type=self.submission_type))
# if hasattr(self.pyd, "csv"):
# export_csv_btn = QPushButton("Export CSV")
# export_csv_btn.setObjectName("export_csv_btn")
# self.layout.addWidget(export_csv_btn)
# export_csv_btn.clicked.connect(self.export_csv_function)
# submit_btn = QPushButton("Submit")
# submit_btn.setObjectName("submit_btn")
# self.layout.addWidget(submit_btn)
# submit_btn.clicked.connect(self.submit_new_sample_function)
# self.setLayout(self.layout)
# self.app.report.add_result(self.report)
# self.app.result_reporter()
def create_widget(self, key:str, value:dict|PydReagent, submission_type:str|None=None, extraction_kit:str|None=None) -> "self.InfoItem": def create_widget(self, key:str, value:dict|PydReagent, submission_type:str|None=None, extraction_kit:str|None=None) -> "self.InfoItem":
""" """
@@ -633,6 +617,11 @@ class SubmissionFormWidget(QWidget):
self.reagent = reagent self.reagent = reagent
self.extraction_kit = extraction_kit self.extraction_kit = extraction_kit
layout = QVBoxLayout() layout = QVBoxLayout()
# layout = QGridLayout()
# self.check_box = QCheckBox(self)
# self.check_box.setChecked(True)
# self.check_box.stateChanged.connect(self.check_uncheck)
# layout.addWidget(self.check_box, 0,0)
self.label = self.ReagentParsedLabel(reagent=reagent) self.label = self.ReagentParsedLabel(reagent=reagent)
layout.addWidget(self.label) layout.addWidget(self.label)
self.lot = self.ReagentLot(reagent=reagent, extraction_kit=extraction_kit) self.lot = self.ReagentLot(reagent=reagent, extraction_kit=extraction_kit)
@@ -645,6 +634,14 @@ class SubmissionFormWidget(QWidget):
# If changed set self.missing to True and update self.label # If changed set self.missing to True and update self.label
self.lot.currentTextChanged.connect(self.updated) self.lot.currentTextChanged.connect(self.updated)
# def check_uncheck(self):
# if self.check_box.isChecked():
# self.lot.setCurrentIndex(0)
# self.lot.setEnabled(True)
# else:
# self.lot.setCurrentText("Not Applicable")
# self.lot.setEnabled(False)
def parse_form(self) -> Tuple[PydReagent, dict]: def parse_form(self) -> Tuple[PydReagent, dict]:
""" """
Pulls form info into PydReagent Pulls form info into PydReagent
@@ -652,6 +649,8 @@ class SubmissionFormWidget(QWidget):
Returns: Returns:
Tuple[PydReagent, dict]: PydReagent and Report(?) Tuple[PydReagent, dict]: PydReagent and Report(?)
""" """
# if not self.check_box.isChecked():
# return None, None
lot = self.lot.currentText() lot = self.lot.currentText()
logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}") logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}")
wanted_reagent = Reagent.query(lot_number=lot, reagent_type=self.reagent.type) wanted_reagent = Reagent.query(lot_number=lot, reagent_type=self.reagent.type)
@@ -671,7 +670,7 @@ class SubmissionFormWidget(QWidget):
rt = ReagentType.query(name=self.reagent.type) rt = ReagentType.query(name=self.reagent.type)
if rt == None: if rt == None:
rt = ReagentType.query(kit_type=self.extraction_kit, reagent=wanted_reagent) rt = ReagentType.query(kit_type=self.extraction_kit, reagent=wanted_reagent)
return PydReagent(name=wanted_reagent.name, lot=wanted_reagent.lot, type=rt.name, expiry=wanted_reagent.expiry, parsed=not self.missing), None return PydReagent(name=wanted_reagent.name, lot=wanted_reagent.lot, type=rt.name, expiry=wanted_reagent.expiry, missing=False), None
def updated(self): def updated(self):
""" """
@@ -736,8 +735,11 @@ class SubmissionFormWidget(QWidget):
looked_up_reg = None looked_up_reg = None
# logger.debug(f"Because there was no reagent listed for {reagent.lot}, we will insert the last lot used: {looked_up_reg}") # logger.debug(f"Because there was no reagent listed for {reagent.lot}, we will insert the last lot used: {looked_up_reg}")
if looked_up_reg != None: if looked_up_reg != None:
relevant_reagents.remove(str(looked_up_reg.lot)) try:
relevant_reagents.insert(0, str(looked_up_reg.lot)) relevant_reagents.remove(str(looked_up_reg.lot))
relevant_reagents.insert(0, str(looked_up_reg.lot))
except ValueError as e:
logger.error(f"Error reordering relevant reagents: {e}")
else: else:
if len(relevant_reagents) > 1: if len(relevant_reagents) > 1:
# logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. Moving to front of list.") # logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. Moving to front of list.")

2
src/submissions/templates/basicsubmission_details.html
View File

@@ -113,7 +113,7 @@
{% endif %} {% endif %}
{% if sub['export_map'] %} {% if sub['export_map'] %}
<h3><u>Plate map:</u></h3> <h3><u>Plate map:</u></h3>
<img height="300px" width="650px" src="data:image/jpeg;base64,{{ sub['export_map'] | safe }}"> <img height="600px" width="1300px" src="data:image/jpeg;base64,{{ sub['export_map'] | safe }}">
{% endif %} {% endif %}
{% endblock %} {% endblock %}
{% if signing_permission %} {% if signing_permission %}

17
src/submissions/tools.py
View File

@@ -14,6 +14,11 @@ from sqlalchemy import create_engine
from pydantic import field_validator, BaseModel, Field from pydantic import field_validator, BaseModel, Field
from pydantic_settings import BaseSettings, SettingsConfigDict from pydantic_settings import BaseSettings, SettingsConfigDict
from typing import Any, Tuple, Literal, List from typing import Any, Tuple, Literal, List
from PyQt6.QtGui import QTextDocument, QPageSize
from PyQt6.QtWebEngineWidgets import QWebEngineView
# from PyQt6 import QtPrintSupport, QtCore, QtWebEngineWidgets
from PyQt6.QtPrintSupport import QPrinter
logger = logging.getLogger(f"submissions.{__name__}") logger = logging.getLogger(f"submissions.{__name__}")
@@ -535,6 +540,18 @@ class Report(BaseModel):
def rreplace(s, old, new): def rreplace(s, old, new):
return (s[::-1].replace(old[::-1],new[::-1], 1))[::-1] return (s[::-1].replace(old[::-1],new[::-1], 1))[::-1]
def html_to_pdf(html, output_file:Path|str):
if isinstance(output_file, str):
output_file = Path(output_file)
# document = QTextDocument()
document = QWebEngineView()
document.setHtml(html)
printer = QPrinter(QPrinter.PrinterMode.HighResolution)
printer.setOutputFormat(QPrinter.OutputFormat.PdfFormat)
printer.setOutputFileName(output_file.absolute().__str__())
printer.setPageSize(QPageSize(QPageSize.PageSizeId.A4))
document.print(printer)
ctx = get_config(None) ctx = get_config(None)
def is_power_user() -> bool: def is_power_user() -> bool: