diff --git a/CHANGELOG.md b/CHANGELOG.md
index 447c4d0..a865960 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,7 @@
+## 202404.04
+
+- Storing of default values in db rather than hardcoded.
+
## 202404.03
- Package updates.
diff --git a/TODO.md b/TODO.md
index 0d87630..a18737c 100644
--- a/TODO.md
+++ b/TODO.md
@@ -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.
- [x] Have sample parser check for controls and add to reagents?
- [x] Update controls to NestedMutableJson
@@ -6,7 +9,7 @@
- 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.
- 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.
- [ ] Merge BasicSubmission.find_subclasses and BasicSubmission.find_polymorphic_subclass
- [x] Fix updating of Extraction Kit in submission form widget.
diff --git a/alembic.ini b/alembic.ini
index 4aedfb1..dceb31e 100644
--- a/alembic.ini
+++ b/alembic.ini
@@ -55,9 +55,9 @@ version_path_separator = os # Use os.pathsep. Default configuration used for ne
# are written from script.py.mako
# 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\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]
diff --git a/alembic/versions/6d2a357860ef_adding_cost_centre_storage_to_.py b/alembic/versions/6d2a357860ef_adding_cost_centre_storage_to_.py
new file mode 100644
index 0000000..93d6e66
--- /dev/null
+++ b/alembic/versions/6d2a357860ef_adding_cost_centre_storage_to_.py
@@ -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 ###
diff --git a/alembic/versions/e6647bd661d9_adding_default_info_to_submissiontype.py b/alembic/versions/e6647bd661d9_adding_default_info_to_submissiontype.py
new file mode 100644
index 0000000..1bd14f5
--- /dev/null
+++ b/alembic/versions/e6647bd661d9_adding_default_info_to_submissiontype.py
@@ -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 ###
diff --git a/src/submissions/backend/db/models/kits.py b/src/submissions/backend/db/models/kits.py
index e7b23de..08ada5a 100644
--- a/src/submissions/backend/db/models/kits.py
+++ b/src/submissions/backend/db/models/kits.py
@@ -374,11 +374,15 @@ class Reagent(BaseClass):
except (TypeError, AttributeError) as e:
place_holder = date.today()
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(
name=self.name,
type=rtype,
lot=self.lot,
- expiry=place_holder.strftime("%Y-%m-%d")
+ expiry=place_holder
)
def update_last_used(self, kit:KitType) -> Report:
@@ -410,6 +414,7 @@ class Reagent(BaseClass):
@classmethod
@setup_lookup
def query(cls,
+ id:int|None=None,
reagent_type:str|ReagentType|None=None,
lot_number: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.
"""
query: Query = cls.__database_session__.query(cls)
+ match id:
+ case int():
+ query = query.filter(cls.id==id)
+ limit = 1
+ case _:
+ pass
match reagent_type:
case str():
# 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
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.
+ defaults = Column(JSON) #: Basic information about this submission type
instances = relationship("BasicSubmission", backref="submission_type") #: Concrete instances of this type.
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.
@@ -653,6 +665,10 @@ class SubmissionType(BaseClass):
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 ]))
+ def get_submission_class(self):
+ from .submissions import BasicSubmission
+ return BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.name)
+
@classmethod
@setup_lookup
def query(cls,
diff --git a/src/submissions/backend/db/models/organizations.py b/src/submissions/backend/db/models/organizations.py
index 9bfcd94..d66a39b 100644
--- a/src/submissions/backend/db/models/organizations.py
+++ b/src/submissions/backend/db/models/organizations.py
@@ -65,8 +65,8 @@ class Organization(BaseClass):
pass
match name:
case str():
- # logger.debug(f"Looking up organization with name: {name}")
- query = query.filter(cls.name==name)
+ # logger.debug(f"Looking up organization with name starting with: {name}")
+ query = query.filter(cls.name.startswith(name))
limit = 1
case _:
pass
diff --git a/src/submissions/backend/db/models/submissions.py b/src/submissions/backend/db/models/submissions.py
index 819451a..913e483 100644
--- a/src/submissions/backend/db/models/submissions.py
+++ b/src/submissions/backend/db/models/submissions.py
@@ -3,12 +3,12 @@ Models for the main submission types.
'''
from __future__ import annotations
from getpass import getuser
-import logging, uuid, tempfile, re, yaml, base64
+import logging, uuid, tempfile, re, yaml, base64, sys
from zipfile import ZipFile
from tempfile import TemporaryDirectory
-from reportlab.graphics.barcode import createBarcodeImageInMemory
-from reportlab.graphics.shapes import Drawing
-from reportlab.lib.units import mm
+# from reportlab.graphics.barcode import createBarcodeImageInMemory
+# from reportlab.graphics.shapes import Drawing
+# from reportlab.lib.units import mm
from operator import attrgetter, itemgetter
from pprint import pformat
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.attributes import flag_modified
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 sqlite3 import OperationalError as SQLOperationalError, IntegrityError as SQLIntegrityError
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
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.
- 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
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(
"SubmissionSampleAssociation",
@@ -103,12 +101,59 @@ class BasicSubmission(BaseClass):
return f"{submission_type}Submission({self.rsl_plate_num})"
@classmethod
- def jsons(cls):
+ def jsons(cls) -> List[str]:
output = [item.name for item in cls.__table__.columns if isinstance(item.type, JSON)]
if issubclass(cls, BasicSubmission) and not cls.__name__ == "BasicSubmission":
output += BasicSubmission.jsons()
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:
"""
Constructs dictionary used in submissions summary
@@ -168,6 +213,11 @@ class BasicSubmission(BaseClass):
logger.debug(f"Attempting reagents.")
try:
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:
logger.error(f"We got an error retrieving reagents: {e}")
reagents = None
@@ -181,10 +231,12 @@ class BasicSubmission(BaseClass):
except Exception as e:
logger.error(f"Error setting equipment: {e}")
equipment = None
+ cost_centre = self.cost_centre
else:
reagents = None
samples = None
equipment = None
+ cost_centre = None
# logger.debug("Getting comments")
try:
comments = self.comment
@@ -198,6 +250,8 @@ class BasicSubmission(BaseClass):
output["extraction_info"] = ext_info
output["comment"] = comments
output["equipment"] = equipment
+ output["Cost Centre"] = cost_centre
+ output["Signed By"] = self.signed_by
return output
def calculate_column_count(self) -> int:
@@ -293,18 +347,18 @@ class BasicSubmission(BaseClass):
"""
return [item.role for item in self.submission_equipment_associations]
- def make_plate_barcode(self, width:int=100, height:int=25) -> Drawing:
- """
- Creates a barcode image for this BasicSubmission.
+ # def make_plate_barcode(self, width:int=100, height:int=25) -> Drawing:
+ # """
+ # Creates a barcode image for this BasicSubmission.
- Args:
- width (int, optional): Width (pixels) of image. Defaults to 100.
- height (int, optional): Height (pixels) of image. Defaults to 25.
+ # Args:
+ # width (int, optional): Width (pixels) of image. Defaults to 100.
+ # height (int, optional): Height (pixels) of image. Defaults to 25.
- Returns:
- Drawing: image object
- """
- return createBarcodeImageInMemory('Code128', value=self.rsl_plate_num, width=width*mm, height=height*mm, humanReadable=True, format="png")
+ # Returns:
+ # Drawing: image object
+ # """
+ # return createBarcodeImageInMemory('Code128', value=self.rsl_plate_num, width=width*mm, height=height*mm, humanReadable=True, format="png")
@classmethod
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():
logger.debug(f"Setting JSON attribute.")
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:
existing = []
if value in existing:
logger.warning("Value already exists. Preventing duplicate addition.")
return
else:
- existing.append(value)
+ if isinstance(value, list):
+ existing += value
+ else:
+ existing.append(value)
self.__setattr__(key, existing)
flag_modified(self, key)
return
@@ -634,7 +694,7 @@ class BasicSubmission(BaseClass):
from backend.validators import RSLNamer
logger.debug(f"instr coming into {cls}: {instr}")
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']
if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]:
data['submission_type'] = defaults['submission_type']
@@ -737,9 +797,7 @@ class BasicSubmission(BaseClass):
Returns:
Tuple(dict, Template): (Updated dictionary, Template to be rendered)
"""
- base_dict['excluded'] = ['excluded', 'reagents', 'samples', 'controls',
- 'extraction_info', 'pcr_info', 'comment',
- 'barcode', 'platemap', 'export_map', 'equipment']
+ base_dict['excluded'] = cls.get_default_info('details_ignore')
env = jinja_template_loading()
temp_name = f"{cls.__name__.lower()}_details.html"
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]
return output
- @classmethod
- def get_default_info(cls) -> dict:
- return dict(abbreviation="BC", submission_type="Bacterial Culture")
+ # @classmethod
+ # def get_default_info(cls) -> dict:
+ # return dict(abbreviation="BC", submission_type="Bacterial Culture")
@classmethod
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
except TypeError as e:
pass
- ext_tech = self.ext_technician or self.technician
- pcr_tech = self.pcr_technician or self.technician
- output['Technician'] = f"Enr: {self.technician}, Ext: {ext_tech}, PCR: {pcr_tech}"
+ if self.ext_technician is None or self.ext_technician == "None":
+ output['Ext Technician'] = self.technician
+ 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
- @classmethod
- def get_default_info(cls) -> dict:
+ # @classmethod
+ # def get_default_info(cls) -> dict:
return dict(abbreviation="WW", submission_type="Wastewater")
@classmethod
@@ -1334,36 +1398,6 @@ class Wastewater(BasicSubmission):
from frontend.widgets import select_open_file
fname = select_open_file(obj=obj, file_extension="xlsx")
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.save(original=False)
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
source_plates = Column(JSON) #: wastewater plates that samples come from
-
__mapper_args__ = dict(polymorphic_identity="Wastewater Artic",
polymorphic_load="inline",
inherit_condition=(id == BasicSubmission.id))
@@ -1411,9 +1444,9 @@ class WastewaterArtic(BasicSubmission):
output['source_plates'] = self.source_plates
return output
- @classmethod
- def get_default_info(cls) -> str:
- return dict(abbreviation="AR", submission_type="Wastewater Artic")
+ # @classmethod
+ # def get_default_info(cls) -> str:
+ # return dict(abbreviation="AR", submission_type="Wastewater Artic")
@classmethod
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
input_dict = super().parse_info(input_dict)
- ws = load_workbook(xl.io, data_only=True)['Egel results']
- data = [ws.cell(row=jj,column=ii) for ii in range(15,27) for jj in range(10,18)]
+ workbook = load_workbook(xl.io, data_only=True)
+ 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]
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 = 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
@classmethod
@@ -1500,34 +1537,38 @@ class WastewaterArtic(BasicSubmission):
Returns:
str: output name
"""
+ logger.debug(f"input string raw: {input_str}")
# Remove letters.
- processed = re.sub(r"[A-Z]", "", input_str)
+ processed = re.sub(r"[A-QS-Z]+\d*", "", input_str)
# Remove trailing '-' if any
processed = processed.strip("-")
+ logger.debug(f"Processed after stripping letters: {processed}")
try:
en_num = re.search(r"\-\d{1}$", processed).group()
processed = rreplace(processed, en_num, "")
except AttributeError:
en_num = "1"
en_num = en_num.strip("-")
- # logger.debug(f"Processed after en-num: {processed}")
+ logger.debug(f"Processed after en-num: {processed}")
try:
- plate_num = re.search(r"\-\d{1}$", processed).group()
+ plate_num = re.search(r"\-\d{1}R?\d?$", processed).group()
processed = rreplace(processed, plate_num, "")
except AttributeError:
plate_num = "1"
plate_num = plate_num.strip("-")
- # logger.debug(f"Processed after plate-num: {processed}")
+ logger.debug(f"Processed after plate-num: {processed}")
day = re.search(r"\d{2}$", processed).group()
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()
processed = rreplace(processed, month, "")
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 = 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
def get_regex(cls) -> str:
@@ -1599,7 +1640,23 @@ class WastewaterArtic(BasicSubmission):
# for jjj, value in enumerate(plate, start=3):
# worksheet.cell(row=iii, column=jjj, value=value)
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:
# logger.debug(f"Gel info check passed.")
if info['gel_info'] != None:
@@ -1618,7 +1675,7 @@ class WastewaterArtic(BasicSubmission):
column = start_column + 2 + jjj
worksheet.cell(row=start_row, column=column, value=kj['name'])
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 info['gel_image'] != None:
worksheet = input_excel['Egel results']
diff --git a/src/submissions/backend/excel/parser.py b/src/submissions/backend/excel/parser.py
index 7c9f2d0..69ed3a6 100644
--- a/src/submissions/backend/excel/parser.py
+++ b/src/submissions/backend/excel/parser.py
@@ -62,9 +62,11 @@ class SheetParser(object):
parser = InfoParser(xl=self.xl, submission_type=self.sub['submission_type']['value'])
info = parser.parse_info()
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():
match k:
case "sample":
+ # case item if
pass
case _:
self.sub[k] = v
@@ -97,9 +99,9 @@ class SheetParser(object):
"""
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']):
- 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():
self.sub['extraction_kit'] = dict(value=dlg.getValues(), missing=True)
else:
@@ -133,7 +135,11 @@ class SheetParser(object):
"""
# logger.debug(f"Submission dictionary coming into 'to_pydantic':\n{pformat(self.sub)}")
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
psm = PydSubmission(filepath=self.filepath, **self.sub)
return psm
@@ -142,11 +148,12 @@ class InfoParser(object):
def __init__(self, xl:pd.ExcelFile, submission_type:str):
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
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.
@@ -156,10 +163,10 @@ class InfoParser(object):
Returns:
dict: Location map of all info for this submission type
"""
- if isinstance(submission_type, str):
- submission_type = dict(value=submission_type, missing=True)
- logger.debug(f"Looking up submission type: {submission_type['value']}")
- submission_type = SubmissionType.query(name=submission_type['value'])
+ if isinstance(self.submission_type, str):
+ self.submission_type = dict(value=self.submission_type, missing=True)
+ logger.debug(f"Looking up submission type: {self.submission_type['value']}")
+ submission_type = SubmissionType.query(name=self.submission_type['value'])
info_map = submission_type.info_map
# Get the parse_info method from the submission type specified
self.custom_parser = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=submission_type.name).parse_info
@@ -172,16 +179,25 @@ class InfoParser(object):
Returns:
dict: key:value of basic info
"""
+ if isinstance(self.submission_type, str):
+ self.submission_type = dict(value=self.submission_type, missing=True)
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:
df = self.xl.parse(sheet, header=None)
relevant = {}
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):
dicto[k] = dict(value=v, missing=False)
continue
- if k in ["samples", "all_sheets"]:
- continue
+ logger.debug(f"Looking for {k} in self.map")
if sheet in self.map[k]['sheets']:
relevant[k] = v
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]
expiry = df.iat[relevant[item]['expiry']['row']-1, relevant[item]['expiry']['column']-1]
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]
else:
comment = ""
@@ -294,7 +311,7 @@ class SampleParser(object):
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}")
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'])
if "plates" in sample_info_map:
self.plates = sample_info_map['plates']
@@ -439,7 +456,7 @@ class SampleParser(object):
"""
result = None
new_samples = []
- logger.debug(f"Starting samples: {pformat(self.samples)}")
+ # logger.debug(f"Starting samples: {pformat(self.samples)}")
for sample in self.samples:
translated_dict = {}
for k, v in sample.items():
diff --git a/src/submissions/backend/validators/__init__.py b/src/submissions/backend/validators/__init__.py
index 8521858..22c0102 100644
--- a/src/submissions/backend/validators/__init__.py
+++ b/src/submissions/backend/validators/__init__.py
@@ -74,8 +74,8 @@ class RSLNamer(object):
check = True
if check:
# logger.debug("Final option, ask the user for submission type")
- from frontend.widgets import SubmissionTypeSelector
- dlg = SubmissionTypeSelector(title="Couldn't parse submission type.", message="Please select submission type from list below.")
+ from frontend.widgets import ObjectSelector
+ dlg = ObjectSelector(title="Couldn't parse submission type.", message="Please select submission type from list below.", obj_type=SubmissionType)
if dlg.exec():
submission_type = dlg.parse_form()
submission_type = submission_type.replace("_", " ")
diff --git a/src/submissions/backend/validators/pydant.py b/src/submissions/backend/validators/pydant.py
index a4a76a7..4d3c64c 100644
--- a/src/submissions/backend/validators/pydant.py
+++ b/src/submissions/backend/validators/pydant.py
@@ -8,13 +8,13 @@ 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, Tuple
+from typing import List, Tuple, Literal
from . import RSLNamer
from pathlib import Path
from tools import check_not_nan, convert_nans_to_nones, Report, Result, row_map
from backend.db.models import *
from sqlalchemy.exc import StatementError, IntegrityError
-from PyQt6.QtWidgets import QComboBox, QWidget
+from PyQt6.QtWidgets import QWidget
from openpyxl import load_workbook, Workbook
from io import BytesIO
@@ -24,7 +24,7 @@ class PydReagent(BaseModel):
lot: str|None
type: str|None
- expiry: date|None
+ expiry: date|Literal['NA']|None
name: str|None
missing: bool = Field(default=True)
comment: str|None = Field(default="", validate_default=True)
@@ -77,6 +77,8 @@ class PydReagent(BaseModel):
match value:
case int():
return datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value - 2).date()
+ case 'NA':
+ return value
case str():
return parse(value)
case date():
@@ -87,6 +89,13 @@ class PydReagent(BaseModel):
value = date.today()
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")
@classmethod
def enforce_name(cls, value, values):
@@ -125,6 +134,10 @@ class PydReagent(BaseModel):
reagent.type.append(reagent_type)
case "comment":
continue
+ case "expiry":
+ if isinstance(value, str):
+ value = date(year=1970, month=1, day=1)
+ reagent.expiry = value
case _:
try:
reagent.__setattr__(key, value)
@@ -271,6 +284,7 @@ class PydSubmission(BaseModel, extra='allow'):
reagents: List[dict]|List[PydReagent] = []
samples: List[PydSample]
equipment: List[PydEquipment]|None =[]
+ cost_centre: dict|None = Field(default=dict(value=None, missing=True), validate_default=True)
@field_validator('equipment', mode='before')
@classmethod
@@ -332,10 +346,28 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("submitting_lab", mode="before")
@classmethod
def rescue_submitting_lab(cls, value):
- if value == None:
+ if value is None:
return dict(value=None, missing=True)
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')
@classmethod
def rescue_rsl_number(cls, value):
@@ -427,6 +459,30 @@ class PydSubmission(BaseModel, extra='allow'):
output.append(sample)
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):
self.__setattr__(name=key, value=value)
@@ -599,6 +655,7 @@ class PydSubmission(BaseModel, extra='allow'):
else:
info = {k:v for k,v in self.improved_dict().items() if isinstance(v, dict)}
reagents = self.reagents
+
if len(reagents + list(info.keys())) == 0:
# logger.warning("No info to fill in, returning")
return None
@@ -616,14 +673,14 @@ class PydSubmission(BaseModel, extra='allow'):
new_reagent = {}
new_reagent['type'] = reagent.type
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']['value'] = reagent.expiry
+ new_reagent['expiry']['value'] = reagent.expiry or "NA"
new_reagent['sheet'] = excel_map[new_reagent['type']]['sheet']
# name is only present for Bacterial Culture
try:
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:
logger.error(f"Couldn't get name due to {e}")
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']}")
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']}")
+ if reagent['expiry']['value'].year == 1970:
+ reagent['expiry']['value'] = "NA"
worksheet.cell(row=reagent['expiry']['row'], column=reagent['expiry']['column'], value=reagent['expiry']['value'])
try:
# 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)}")
if isinstance(extraction_kit, str):
extraction_kit = dict(value=extraction_kit)
- if extraction_kit is not None:
- if extraction_kit != self.extraction_kit['value']:
+ if extraction_kit is not None and extraction_kit != self.extraction_kit['value']:
self.extraction_kit['value'] = extraction_kit['value']
- reagenttypes = []
- else:
- reagenttypes = [item.type for item in self.reagents]
- else:
- reagenttypes = [item.type for item in self.reagents]
+ # reagenttypes = []
+ # else:
+ # reagenttypes = [item.type for item in self.reagents]
+ # else:
+ # reagenttypes = [item.type for item in self.reagents]
logger.debug(f"Looking up {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'])]
@@ -808,21 +866,26 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug(f"Checking if reagents match kit contents: {check}")
# # what reagent types are in both lists?
# missing = list(set(ext_kit_rtypes).difference(reagenttypes))
- missing = []
- output_reagents = self.reagents
- # output_reagents = ext_kit_rtypes
- logger.debug(f"Already have these reagent types: {reagenttypes}")
- for rt in ext_kit_rtypes:
- if rt.type not in reagenttypes:
- missing.append(rt)
- if rt.type not in [item.type for item in output_reagents]:
- output_reagents.append(rt)
- logger.debug(f"Missing reagents types: {missing}")
+ # missing = []
+ # Exclude any reagenttype found in this pyd not expected in kit.
+ expected_check = [item.type for item in ext_kit_rtypes]
+ output_reagents = [rt for rt in self.reagents if rt.type in expected_check]
+ logger.debug(f"Already have these reagent types: {output_reagents}")
+ missing_check = [item.type for item in output_reagents]
+ missing_reagents = [rt for rt in ext_kit_rtypes if rt.type not in missing_check]
+ missing_reagents += [rt for rt in output_reagents if rt.missing]
+ # for rt in ext_kit_rtypes:
+ # 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 len(missing)==0:
+ if len(missing_reagents)==0:
result = None
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)
return output_reagents, report
diff --git a/src/submissions/frontend/widgets/misc.py b/src/submissions/frontend/widgets/misc.py
index aef9234..a802b3c 100644
--- a/src/submissions/frontend/widgets/misc.py
+++ b/src/submissions/frontend/widgets/misc.py
@@ -85,10 +85,10 @@ class AddReagentForm(QDialog):
Returns:
dict: Output info
"""
- return dict(name=self.name_input.currentText(),
- lot=self.lot_input.text(),
+ return dict(name=self.name_input.currentText().strip(),
+ lot=self.lot_input.text().strip(),
expiry=self.exp_input.date().toPyDate(),
- type=self.type_input.currentText())
+ type=self.type_input.currentText().strip())
def update_names(self):
"""
diff --git a/src/submissions/frontend/widgets/pop_ups.py b/src/submissions/frontend/widgets/pop_ups.py
index b3bd598..414e2aa 100644
--- a/src/submissions/frontend/widgets/pop_ups.py
+++ b/src/submissions/frontend/widgets/pop_ups.py
@@ -7,7 +7,7 @@ from PyQt6.QtWidgets import (
)
from tools import jinja_template_loading
import logging
-from backend.db.models import KitType, SubmissionType
+from backend.db import models
from typing import Literal
logger = logging.getLogger(f"submissions.{__name__}")
@@ -45,16 +45,18 @@ class AlertPop(QMessageBox):
self.setInformativeText(message)
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__()
self.setWindowTitle(title)
self.widget = QComboBox()
- kits = [item.name for item in KitType.query()]
- self.widget.addItems(kits)
+ if isinstance(obj_type, str):
+ 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)
# set yes/no buttons
QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
@@ -78,36 +80,69 @@ class KitSelector(QDialog):
"""
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)
+# class KitSelector(QDialog):
+# """
+# dialog to input KitType manually
+# """
+# def __init__(self, title:str, message:str) -> QDialog:
+# super().__init__()
+# self.setWindowTitle(title)
+# self.widget = QComboBox()
+# kits = [item.name for item in KitType.query()]
+# self.widget.addItems(kits)
+# 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
+# def getValues(self) -> str:
+# """
+# Get KitType(str) from widget
- Returns:
- str: SubmissionType as str
- """
- return self.widget.currentText()
+# Returns:
+# str: KitType as str
+# """
+# 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()
diff --git a/src/submissions/frontend/widgets/submission_details.py b/src/submissions/frontend/widgets/submission_details.py
index 9cd9ac8..2a1b7db 100644
--- a/src/submissions/frontend/widgets/submission_details.py
+++ b/src/submissions/frontend/widgets/submission_details.py
@@ -5,12 +5,12 @@ from PyQt6.QtWebChannel import QWebChannel
from PyQt6.QtCore import Qt, pyqtSlot
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 io import BytesIO
from tempfile import TemporaryFile, TemporaryDirectory
from pathlib import Path
-from xhtml2pdf import pisa
+# from xhtml2pdf import pisa
import logging, base64
from getpass import getuser
from datetime import datetime
@@ -54,6 +54,7 @@ class SubmissionDetails(QDialog):
self.channel = QWebChannel()
self.channel.registerObject('backend', self)
self.submission_details(submission=sub)
+ self.rsl_plate_num = sub.rsl_plate_num
self.webview.page().setWebChannel(self.channel)
@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'})}")
# don't want id
del self.base_dict['id']
- logger.debug(f"Creating barcode.")
- if not check_if_app():
- self.base_dict['barcode'] = base64.b64encode(submission.make_plate_barcode(width=120, height=30)).decode('utf-8')
+ # logger.debug(f"Creating barcode.")
+ # if not check_if_app():
+ # self.base_dict['barcode'] = base64.b64encode(submission.make_plate_barcode(width=120, height=30)).decode('utf-8')
logger.debug(f"Making platemap...")
self.base_dict['platemap'] = submission.make_plate_map()
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()})")
if isinstance(submission, str):
submission = BasicSubmission.query(rsl_number=submission)
- submission.uploaded_by = getuser()
+ submission.signed_by = getuser()
submission.save()
+ self.submission_details(submission=self.rsl_plate_num)
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")
image_io = BytesIO()
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)
screenshot = hti.screenshot(self.base_dict['platemap'], save_as=temp_file.name)
export_map = Image.open(screenshot[0])
@@ -126,8 +128,9 @@ class SubmissionDetails(QDialog):
del self.base_dict['platemap']
self.html2 = self.template.render(sub=self.base_dict)
try:
- with open(fname, "w+b") as f:
- pisa.CreatePDF(self.html2, dest=f)
+ # with open(fname, "w+b") as f:
+ # pisa.CreatePDF(self.html2, dest=f)
+ html_to_pdf(html=self.html2, output_file=fname)
except PermissionError as e:
logger.error(f"Error saving pdf: {e}")
msg = QMessageBox()
diff --git a/src/submissions/frontend/widgets/submission_table.py b/src/submissions/frontend/widgets/submission_table.py
index 215ae7d..891b8b1 100644
--- a/src/submissions/frontend/widgets/submission_table.py
+++ b/src/submissions/frontend/widgets/submission_table.py
@@ -8,8 +8,8 @@ from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
from PyQt6.QtGui import QAction, QCursor
from backend.db.models import BasicSubmission
from backend.excel import make_report_html, make_report_xlsx
-from tools import Report, Result, row_map, get_first_blank_df_row
-from xhtml2pdf import pisa
+from tools import Report, Result, row_map, get_first_blank_df_row, html_to_pdf
+# from xhtml2pdf import pisa
from .functions import select_save_file, select_open_file
from .misc import ReportDatePicker
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'])
# 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")
- with open(fname, "w+b") as f:
- pisa.CreatePDF(html, dest=f)
+ # with open(fname, "w+b") as f:
+ # pisa.CreatePDF(html, dest=f)
+ html_to_pdf(html=html, output_file=fname)
writer = pd.ExcelWriter(fname.with_suffix(".xlsx"), engine='openpyxl')
summary_df.to_excel(writer, sheet_name="Report")
detailed_df.to_excel(writer, sheet_name="Details", index=False)
diff --git a/src/submissions/frontend/widgets/submission_widget.py b/src/submissions/frontend/widgets/submission_widget.py
index 07babe9..50ee364 100644
--- a/src/submissions/frontend/widgets/submission_widget.py
+++ b/src/submissions/frontend/widgets/submission_widget.py
@@ -135,7 +135,7 @@ class SubmissionFormContainer(QWidget):
info = dlg.parse_form()
logger.debug(f"Reagent info: {info}")
# create reagent object
- reagent = PydReagent(ctx=self.app.ctx, **info)
+ reagent = PydReagent(ctx=self.app.ctx, **info, missing=False)
# send reagent to db
sqlobj, result = reagent.toSQL()
sqlobj.save()
@@ -150,45 +150,29 @@ class SubmissionFormWidget(QWidget):
# self.report = Report()
self.app = parent.app
self.pyd = submission
- # self.input = [{k:v} for k,v in kwargs.items()]
- # self.samples = []
self.missing_info = []
- self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx', 'comment',
- 'equipment', 'gel_controls', 'id', 'cost', 'extraction_info',
- 'controls', 'pcr_info', 'gel_info', 'gel_image']
- self.recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
+ st = SubmissionType.query(name=self.pyd.submission_type['value']).get_submission_class()
+ defaults = st.get_default_info("form_recover", "form_ignore")
+ self.recover = defaults['form_recover']
+ 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()
# for k, v in kwargs.items():
for k in list(self.pyd.model_fields.keys()) + list(self.pyd.model_extra.keys()):
- if k not in self.ignore:
- try:
- value = self.pyd.__getattribute__(k)
- except AttributeError:
- logger.error(f"Couldn't get attribute from pyd: {k}")
- value = dict(value=None, missing=True)
- add_widget = self.create_widget(key=k, value=value, submission_type=self.pyd.submission_type['value'])
- if add_widget != None:
- self.layout.addWidget(add_widget)
- if k == "extraction_kit":
- add_widget.input.currentTextChanged.connect(self.scrape_reagents)
- # else:
- # self.__setattr__(k, v)
- # self.scrape_reagents(self.extraction_kit['value'])
+ if k in self.ignore:
+ continue
+ try:
+ value = self.pyd.__getattribute__(k)
+ except AttributeError:
+ logger.error(f"Couldn't get attribute from pyd: {k}")
+ value = dict(value=None, missing=True)
+ add_widget = self.create_widget(key=k, value=value, submission_type=self.pyd.submission_type['value'])
+ if add_widget != None:
+ self.layout.addWidget(add_widget)
+ if k == "extraction_kit":
+ add_widget.input.currentTextChanged.connect(self.scrape_reagents)
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":
"""
@@ -633,6 +617,11 @@ class SubmissionFormWidget(QWidget):
self.reagent = reagent
self.extraction_kit = extraction_kit
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)
layout.addWidget(self.label)
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
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]:
"""
Pulls form info into PydReagent
@@ -652,6 +649,8 @@ class SubmissionFormWidget(QWidget):
Returns:
Tuple[PydReagent, dict]: PydReagent and Report(?)
"""
+ # if not self.check_box.isChecked():
+ # return None, None
lot = self.lot.currentText()
logger.debug(f"Using this lot for the reagent {self.reagent}: {lot}")
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)
if rt == None:
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):
"""
@@ -736,8 +735,11 @@ class SubmissionFormWidget(QWidget):
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}")
if looked_up_reg != None:
- relevant_reagents.remove(str(looked_up_reg.lot))
- relevant_reagents.insert(0, str(looked_up_reg.lot))
+ try:
+ 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:
if len(relevant_reagents) > 1:
# logger.debug(f"Found {reagent.lot} in relevant reagents: {relevant_reagents}. Moving to front of list.")
diff --git a/src/submissions/templates/basicsubmission_details.html b/src/submissions/templates/basicsubmission_details.html
index c07d256..ceae5bf 100644
--- a/src/submissions/templates/basicsubmission_details.html
+++ b/src/submissions/templates/basicsubmission_details.html
@@ -113,7 +113,7 @@
{% endif %}
{% if sub['export_map'] %}
Plate map:
- 
+
{% endif %}
{% endblock %}
{% if signing_permission %}
diff --git a/src/submissions/tools.py b/src/submissions/tools.py
index 8bbb35d..b279ef5 100644
--- a/src/submissions/tools.py
+++ b/src/submissions/tools.py
@@ -14,6 +14,11 @@ from sqlalchemy import create_engine
from pydantic import field_validator, BaseModel, Field
from pydantic_settings import BaseSettings, SettingsConfigDict
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__}")
@@ -535,6 +540,18 @@ class Report(BaseModel):
def rreplace(s, old, new):
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)
def is_power_user() -> bool: