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Added in ability to overwrite submissions.

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This commit is contained in:
Landon Wark
2023-01-26 14:54:32 -06:00
parent 3c308f6559
commit bbb65d3fe6
9 changed files with 151 additions and 93 deletions
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2
alembic.ini
View File

@@ -55,7 +55,7 @@ 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:///submissions.db sqlalchemy.url = sqlite:///L:\Robotics Laboratory Support\Submissions\submissions.db
[post_write_hooks] [post_write_hooks]

36
alembic/versions/03da9270e51f_initial_commit.py → alembic/versions/8753ed70f148_initial_commit.py
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@@ -1,8 +1,8 @@
"""initial commit """initial commit
Revision ID: 03da9270e51f Revision ID: 8753ed70f148
Revises: Revises:
Create Date: 2023-01-19 09:01:03.022482 Create Date: 2023-01-26 12:48:42.340619
""" """
from alembic import op from alembic import op
@@ -10,7 +10,7 @@ import sqlalchemy as sa
# revision identifiers, used by Alembic. # revision identifiers, used by Alembic.
revision = '03da9270e51f' revision = '8753ed70f148'
down_revision = None down_revision = None
branch_labels = None branch_labels = None
depends_on = None depends_on = None
@@ -50,18 +50,6 @@ def upgrade() -> None:
sa.ForeignKeyConstraint(['kit_id'], ['_kits.id'], name='fk_RT_kits_id', ondelete='SET NULL', use_alter=True), sa.ForeignKeyConstraint(['kit_id'], ['_kits.id'], name='fk_RT_kits_id', ondelete='SET NULL', use_alter=True),
sa.PrimaryKeyConstraint('id') sa.PrimaryKeyConstraint('id')
) )
op.create_table('_control_samples',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('parent_id', sa.String(), nullable=True),
sa.Column('name', sa.String(length=255), nullable=True),
sa.Column('submitted_date', sa.TIMESTAMP(), nullable=True),
sa.Column('contains', sa.JSON(), nullable=True),
sa.Column('matches', sa.JSON(), nullable=True),
sa.Column('kraken', sa.JSON(), nullable=True),
sa.ForeignKeyConstraint(['parent_id'], ['_control_types.id'], name='fk_control_parent_id'),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('name')
)
op.create_table('_organizations', op.create_table('_organizations',
sa.Column('id', sa.INTEGER(), nullable=False), sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('name', sa.String(length=64), nullable=True), sa.Column('name', sa.String(length=64), nullable=True),
@@ -102,8 +90,6 @@ def upgrade() -> None:
sa.Column('submission_type', sa.String(length=32), nullable=True), sa.Column('submission_type', sa.String(length=32), nullable=True),
sa.Column('technician', sa.String(length=64), nullable=True), sa.Column('technician', sa.String(length=64), nullable=True),
sa.Column('reagents_id', sa.String(), nullable=True), sa.Column('reagents_id', sa.String(), nullable=True),
sa.Column('control_id', sa.INTEGER(), nullable=True),
sa.ForeignKeyConstraint(['control_id'], ['_control_samples.id'], name='fk_BC_control_id', ondelete='SET NULL'),
sa.ForeignKeyConstraint(['extraction_kit_id'], ['_kits.id'], name='fk_BS_extkit_id', ondelete='SET NULL'), sa.ForeignKeyConstraint(['extraction_kit_id'], ['_kits.id'], name='fk_BS_extkit_id', ondelete='SET NULL'),
sa.ForeignKeyConstraint(['reagents_id'], ['_reagents.id'], name='fk_BS_reagents_id', ondelete='SET NULL'), sa.ForeignKeyConstraint(['reagents_id'], ['_reagents.id'], name='fk_BS_reagents_id', ondelete='SET NULL'),
sa.ForeignKeyConstraint(['submitting_lab_id'], ['_organizations.id'], name='fk_BS_sublab_id', ondelete='SET NULL'), sa.ForeignKeyConstraint(['submitting_lab_id'], ['_organizations.id'], name='fk_BS_sublab_id', ondelete='SET NULL'),
@@ -121,6 +107,20 @@ def upgrade() -> None:
sa.ForeignKeyConstraint(['rsl_plate_id'], ['_submissions.id'], name='fk_BCS_sample_id', ondelete='SET NULL'), sa.ForeignKeyConstraint(['rsl_plate_id'], ['_submissions.id'], name='fk_BCS_sample_id', ondelete='SET NULL'),
sa.PrimaryKeyConstraint('id') sa.PrimaryKeyConstraint('id')
) )
op.create_table('_control_samples',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('parent_id', sa.String(), nullable=True),
sa.Column('name', sa.String(length=255), nullable=True),
sa.Column('submitted_date', sa.TIMESTAMP(), nullable=True),
sa.Column('contains', sa.JSON(), nullable=True),
sa.Column('matches', sa.JSON(), nullable=True),
sa.Column('kraken', sa.JSON(), nullable=True),
sa.Column('submission_id', sa.INTEGER(), nullable=True),
sa.ForeignKeyConstraint(['parent_id'], ['_control_types.id'], name='fk_control_parent_id'),
sa.ForeignKeyConstraint(['submission_id'], ['_submissions.id'], ),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('name')
)
op.create_table('_reagents_submissions', op.create_table('_reagents_submissions',
sa.Column('reagent_id', sa.INTEGER(), nullable=True), sa.Column('reagent_id', sa.INTEGER(), nullable=True),
sa.Column('submission_id', sa.INTEGER(), nullable=True), sa.Column('submission_id', sa.INTEGER(), nullable=True),
@@ -153,13 +153,13 @@ def downgrade() -> None:
# ### commands auto generated by Alembic - please adjust! ### # ### commands auto generated by Alembic - please adjust! ###
op.drop_table('_ww_samples') op.drop_table('_ww_samples')
op.drop_table('_reagents_submissions') op.drop_table('_reagents_submissions')
op.drop_table('_control_samples')
op.drop_table('_bc_samples') op.drop_table('_bc_samples')
op.drop_table('_submissions') op.drop_table('_submissions')
op.drop_table('_orgs_contacts') op.drop_table('_orgs_contacts')
op.drop_table('_reagentstypes_kittypes') op.drop_table('_reagentstypes_kittypes')
op.drop_table('_reagents') op.drop_table('_reagents')
op.drop_table('_organizations') op.drop_table('_organizations')
op.drop_table('_control_samples')
op.drop_table('_reagent_types') op.drop_table('_reagent_types')
op.drop_table('_kits') op.drop_table('_kits')
op.drop_table('_control_types') op.drop_table('_control_types')

51
src/submissions/backend/db/__init__.py
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@@ -1,7 +1,9 @@
from . import models from . import models
import pandas as pd import pandas as pd
# from sqlite3 import IntegrityError import sqlalchemy.exc
from sqlalchemy.exc import IntegrityError import sqlite3
# from sqlalchemy.exc import IntegrityError, OperationalError
# from sqlite3 import IntegrityError, OperationalError
import logging import logging
from datetime import date, datetime from datetime import date, datetime
from sqlalchemy import and_ from sqlalchemy import and_
@@ -19,48 +21,69 @@ def get_kits_by_use( ctx:dict, kittype_str:str|None) -> list:
def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None: def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None:
logger.debug(f"Hello from store_submission")
for sample in base_submission.samples: for sample in base_submission.samples:
sample.rsl_plate = base_submission sample.rsl_plate = base_submission
logger.debug(f"Attempting to add sample: {sample.to_string()}")
try: try:
ctx['database_session'].add(sample) ctx['database_session'].add(sample)
except IntegrityError: except (sqlite3.IntegrityError, sqlalchemy.exc.IntegrityError) as e:
logger.debug(f"Hit an integrity error : {e}")
continue continue
ctx['database_session'].add(base_submission) ctx['database_session'].add(base_submission)
logger.debug(f"Attempting to add submission: {base_submission.rsl_plate_num}")
try: try:
ctx['database_session'].commit() ctx['database_session'].commit()
except IntegrityError: except (sqlite3.IntegrityError, sqlalchemy.exc.IntegrityError) as e:
logger.debug(f"Hit an integrity error : {e}")
ctx['database_session'].rollback() ctx['database_session'].rollback()
return {"message":"This plate number already exists, so we can't add it."} return {"message":"This plate number already exists, so we can't add it."}
except (sqlite3.OperationalError, sqlalchemy.exc.IntegrityError) as e:
logger.debug(f"Hit an operational error: {e}")
ctx['database_session'].rollback()
return {"message":"The database is locked for editing."}
return None return None
def store_reagent(ctx:dict, reagent:models.Reagent) -> None: def store_reagent(ctx:dict, reagent:models.Reagent) -> None:
logger.debug(reagent.__dict__) logger.debug(reagent.__dict__)
ctx['database_session'].add(reagent) ctx['database_session'].add(reagent)
ctx['database_session'].commit() try:
ctx['database_session'].commit()
except OperationalError:
return {"message":"The database is locked for editing."}
def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmission: def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmission:
query = info_dict['submission_type'].replace(" ", "") query = info_dict['submission_type'].replace(" ", "")
instance = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num==info_dict['rsl_plate_num']).first()
msg = "This submission already exists.\nWould you like to overwrite?"
model = getattr(models, query) model = getattr(models, query)
info_dict['submission_type'] = info_dict['submission_type'].replace(" ", "_").lower() info_dict['submission_type'] = info_dict['submission_type'].replace(" ", "_").lower()
instance = model() if instance == None:
instance = model()
msg = None
for item in info_dict: for item in info_dict:
logger.debug(f"Setting {item} to {info_dict[item]}") logger.debug(f"Setting {item} to {info_dict[item]}")
match item: match item:
case "extraction_kit": case "extraction_kit":
q_str = info_dict[item] q_str = info_dict[item]
logger.debug(f"Looking up kit {q_str}") logger.debug(f"Looking up kit {q_str}")
field_value = lookup_kittype_by_name(ctx=ctx, name=q_str) try:
field_value = lookup_kittype_by_name(ctx=ctx, name=q_str)
except (sqlite3.IntegrityError, sqlalchemy.exc.IntegrityError) as e:
logger.error(f"Hit an integrity error: {e}")
logger.debug(f"Got {field_value} for kit {q_str}") logger.debug(f"Got {field_value} for kit {q_str}")
case "submitting_lab": case "submitting_lab":
q_str = info_dict[item].replace(" ", "_").lower() q_str = info_dict[item].replace(" ", "_").lower()
logger.debug(f"looking up organization: {q_str}") logger.debug(f"Looking up organization: {q_str}")
field_value = lookup_org_by_name(ctx=ctx, name=q_str) field_value = lookup_org_by_name(ctx=ctx, name=q_str)
logger.debug(f"Got {field_value} for organization {q_str}") logger.debug(f"Got {field_value} for organization {q_str}")
case "submitter_plate_num": case "submitter_plate_num":
# Because of unique constraint, the submitter plate number cannot be None, so... # Because of unique constraint, the submitter plate number cannot be None, so...
if info_dict[item] == None: logger.debug(f"Submitter plate id: {info_dict[item]}")
if info_dict[item] == None or info_dict[item] == "None":
logger.debug(f"Got None as a submitter plate number, inserting random string to preserve database unique constraint.")
info_dict[item] = uuid.uuid4().hex.upper() info_dict[item] = uuid.uuid4().hex.upper()
field_value = info_dict[item] field_value = info_dict[item]
# case "samples": # case "samples":
@@ -75,7 +98,9 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
logger.debug(f"Could not set attribute: {item} to {info_dict[item]}") logger.debug(f"Could not set attribute: {item} to {info_dict[item]}")
continue continue
# logger.debug(instance.__dict__) # logger.debug(instance.__dict__)
return instance logger.debug(f"Constructed instance: {instance.to_string()}")
logger.debug(msg)
return instance, {'message':msg}
# looked_up = [] # looked_up = []
# for reagent in reagents: # for reagent in reagents:
# my_reagent = lookup_reagent(reagent) # my_reagent = lookup_reagent(reagent)
@@ -235,7 +260,11 @@ def lookup_all_sample_types(ctx:dict) -> list[str]:
def get_all_available_modes(ctx:dict) -> list[str]: def get_all_available_modes(ctx:dict) -> list[str]:
rel = ctx['database_session'].query(models.Control).first() rel = ctx['database_session'].query(models.Control).first()
cols = [item.name for item in list(rel.__table__.columns) if isinstance(item.type, JSON)] try:
cols = [item.name for item in list(rel.__table__.columns) if isinstance(item.type, JSON)]
except AttributeError as e:
logger.debug(f"Failed to get available modes from db: {e}")
cols = []
return cols return cols

3
src/submissions/backend/db/models/controls.py
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@@ -32,5 +32,6 @@ class Control(Base):
matches = Column(JSON) #: unstructured hashes in matches.tsv for each organism matches = Column(JSON) #: unstructured hashes in matches.tsv for each organism
kraken = Column(JSON) #: unstructured output from kraken_report kraken = Column(JSON) #: unstructured output from kraken_report
# UniqueConstraint('name', name='uq_control_name') # UniqueConstraint('name', name='uq_control_name')
submissions = relationship("BacterialCulture", back_populates="control") submission_id = Column(INTEGER, ForeignKey("_submissions.id"))
submission = relationship("BacterialCulture", back_populates="controls", foreign_keys=[submission_id])

7
src/submissions/backend/db/models/submissions.py
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@@ -30,6 +30,9 @@ class BasicSubmission(Base):
"with_polymorphic": "*", "with_polymorphic": "*",
} }
def to_string(self):
return f"{self.rsl_plate_num} - {self.submitter_plate_num}"
def to_dict(self): def to_dict(self):
try: try:
sub_lab = self.submitting_lab.name sub_lab = self.submitting_lab.name
@@ -90,8 +93,8 @@ class BasicSubmission(Base):
# Below are the custom submission # Below are the custom submission
class BacterialCulture(BasicSubmission): class BacterialCulture(BasicSubmission):
control = relationship("Control", back_populates="submissions") #: A control sample added to submission # control_id = Column(INTEGER, ForeignKey("_control_samples.id", ondelete="SET NULL", name="fk_BC_control_id"))
control_id = Column(INTEGER, ForeignKey("_control_samples.id", ondelete="SET NULL", name="fk_BC_control_id")) controls = relationship("Control", back_populates="submission", uselist=True) #: A control sample added to submission
samples = relationship("BCSample", back_populates="rsl_plate", uselist=True) samples = relationship("BCSample", back_populates="rsl_plate", uselist=True)
# bc_sample_id = Column(INTEGER, ForeignKey("_bc_samples.id", ondelete="SET NULL", name="fk_BC_sample_id")) # bc_sample_id = Column(INTEGER, ForeignKey("_bc_samples.id", ondelete="SET NULL", name="fk_BC_sample_id"))
__mapper_args__ = {"polymorphic_identity": "bacterial_culture", "polymorphic_load": "inline"} __mapper_args__ = {"polymorphic_identity": "bacterial_culture", "polymorphic_load": "inline"}

80
src/submissions/backend/excel/parser.py
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@@ -45,13 +45,14 @@ class SheetParser(object):
def _parse_generic(self, sheet_name:str): def _parse_generic(self, sheet_name:str):
submission_info = self.xl.parse(sheet_name=sheet_name) submission_info = self.xl.parse(sheet_name=sheet_name, dtype=object)
self.sub['submitter_plate_num'] = submission_info.iloc[0][1]
self.sub['rsl_plate_num'] = str(submission_info.iloc[10][1]) self.sub['submitter_plate_num'] = submission_info.iloc[0][1] #if pd.isnull(submission_info.iloc[0][1]) else string_formatter(submission_info.iloc[0][1])
self.sub['submitted_date'] = submission_info.iloc[1][1].date()#.strftime("%Y-%m-%d") self.sub['rsl_plate_num'] = submission_info.iloc[10][1] #if pd.isnull(submission_info.iloc[10][1]) else string_formatter(submission_info.iloc[10][1])
self.sub['submitting_lab'] = submission_info.iloc[0][3] self.sub['submitted_date'] = submission_info.iloc[1][1] #if pd.isnull(submission_info.iloc[1][1]) else submission_info.iloc[1][1].date()#.strftime("%Y-%m-%d")
self.sub['sample_count'] = str(submission_info.iloc[2][3]) self.sub['submitting_lab'] = submission_info.iloc[0][3] #if pd.isnull(submission_info.iloc[0][3]) else string_formatter(submission_info.iloc[0][3])
self.sub['extraction_kit'] = submission_info.iloc[3][3] self.sub['sample_count'] = submission_info.iloc[2][3] #if pd.isnull(submission_info.iloc[2][3]) else string_formatter(submission_info.iloc[2][3])
self.sub['extraction_kit'] = submission_info.iloc[3][3] #if #pd.isnull(submission_info.iloc[3][3]) else string_formatter(submission_info.iloc[3][3])
return submission_info return submission_info
@@ -67,16 +68,17 @@ class SheetParser(object):
tech = ", ".join(tech_reg.findall(tech)) tech = ", ".join(tech_reg.findall(tech))
self.sub['technician'] = tech self.sub['technician'] = tech
# reagents # reagents
self.sub['lot_wash_1'] = submission_info.iloc[1][6]
self.sub['lot_wash_2'] = submission_info.iloc[2][6] self.sub['lot_wash_1'] = submission_info.iloc[1][6] #if pd.isnull(submission_info.iloc[1][6]) else string_formatter(submission_info.iloc[1][6])
self.sub['lot_binding_buffer'] = submission_info.iloc[3][6] self.sub['lot_wash_2'] = submission_info.iloc[2][6] #if pd.isnull(submission_info.iloc[2][6]) else string_formatter(submission_info.iloc[2][6])
self.sub['lot_magnetic_beads'] = submission_info.iloc[4][6] self.sub['lot_binding_buffer'] = submission_info.iloc[3][6] #if pd.isnull(submission_info.iloc[3][6]) else string_formatter(submission_info.iloc[3][6])
self.sub['lot_lysis_buffer'] = submission_info.iloc[5][6] self.sub['lot_magnetic_beads'] = submission_info.iloc[4][6] #if pd.isnull(submission_info.iloc[4][6]) else string_formatter(submission_info.iloc[4][6])
self.sub['lot_elution_buffer'] = submission_info.iloc[6][6] self.sub['lot_lysis_buffer'] = submission_info.iloc[5][6] #if np.nan(submission_info.iloc[5][6]) else string_formatter(submission_info.iloc[5][6])
self.sub['lot_isopropanol'] = submission_info.iloc[9][6] self.sub['lot_elution_buffer'] = submission_info.iloc[6][6] #if pd.isnull(submission_info.iloc[6][6]) else string_formatter(submission_info.iloc[6][6])
self.sub['lot_ethanol'] = submission_info.iloc[10][6] self.sub['lot_isopropanol'] = submission_info.iloc[9][6] #if pd.isnull(submission_info.iloc[9][6]) else string_formatter(submission_info.iloc[9][6])
self.sub['lot_positive_control'] = submission_info.iloc[103][1] self.sub['lot_ethanol'] = submission_info.iloc[10][6] #if pd.isnull(submission_info.iloc[10][6]) else string_formatter(submission_info.iloc[10][6])
self.sub['lot_plate'] = submission_info.iloc[12][6] self.sub['lot_positive_control'] = submission_info.iloc[103][1] #if pd.isnull(submission_info.iloc[103][1]) else string_formatter(submission_info.iloc[103][1])
self.sub['lot_plate'] = submission_info.iloc[12][6] #if pd.isnull(submission_info.iloc[12][6]) else string_formatter(submission_info.iloc[12][6])
sample_parser = SampleParser(submission_info.iloc[15:111]) sample_parser = SampleParser(submission_info.iloc[15:111])
sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples") sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
logger.debug(f"Parser result: {self.sub}") logger.debug(f"Parser result: {self.sub}")
@@ -86,25 +88,26 @@ class SheetParser(object):
def _parse_wastewater(self): def _parse_wastewater(self):
# submission_info = self.xl.parse("WW Submissions (ENTER HERE)") # submission_info = self.xl.parse("WW Submissions (ENTER HERE)")
submission_info = self._parse_generic("WW Submissions (ENTER HERE)") submission_info = self._parse_generic("WW Submissions (ENTER HERE)")
enrichment_info = self.xl.parse("Enrichment Worksheet") enrichment_info = self.xl.parse("Enrichment Worksheet", dtype=object)
extraction_info = self.xl.parse("Extraction Worksheet") extraction_info = self.xl.parse("Extraction Worksheet", dtype=object)
qprc_info = self.xl.parse("qPCR Worksheet") qprc_info = self.xl.parse("qPCR Worksheet", dtype=object)
self.sub['technician'] = f"Enr: {enrichment_info.columns[2]}, Ext: {extraction_info.columns[2]}, PCR: {qprc_info.columns[2]}" self.sub['technician'] = f"Enr: {enrichment_info.columns[2]}, Ext: {extraction_info.columns[2]}, PCR: {qprc_info.columns[2]}"
# reagents # reagents
self.sub['lot_lysis_buffer'] = enrichment_info.iloc[0][14] logger.debug(qprc_info)
self.sub['lot_proteinase_K'] = enrichment_info.iloc[1][14] self.sub['lot_lysis_buffer'] = enrichment_info.iloc[0][14] #if pd.isnull(enrichment_info.iloc[0][14]) else string_formatter(enrichment_info.iloc[0][14])
self.sub['lot_magnetic_virus_particles'] = enrichment_info.iloc[2][14] self.sub['lot_proteinase_K'] = enrichment_info.iloc[1][14] #if pd.isnull(enrichment_info.iloc[1][14]) else string_formatter(enrichment_info.iloc[1][14])
self.sub['lot_enrichment_reagent_1'] = enrichment_info.iloc[3][14] self.sub['lot_magnetic_virus_particles'] = enrichment_info.iloc[2][14] #if pd.isnull(enrichment_info.iloc[2][14]) else string_formatter(enrichment_info.iloc[2][14])
self.sub['lot_binding_buffer'] = extraction_info.iloc[0][14] self.sub['lot_enrichment_reagent_1'] = enrichment_info.iloc[3][14] #if pd.isnull(enrichment_info.iloc[3][14]) else string_formatter(enrichment_info.iloc[3][14])
self.sub['lot_magnetic_beads'] = extraction_info.iloc[1][14] self.sub['lot_binding_buffer'] = extraction_info.iloc[0][14] #if pd.isnull(extraction_info.iloc[0][14]) else string_formatter(extraction_info.iloc[0][14])
self.sub['lot_wash'] = extraction_info.iloc[2][14] self.sub['lot_magnetic_beads'] = extraction_info.iloc[1][14] #if pd.isnull(extraction_info.iloc[1][14]) else string_formatter(extraction_info.iloc[1][14])
self.sub['lot_ethanol'] = extraction_info.iloc[3][14] self.sub['lot_wash'] = extraction_info.iloc[2][14] #if pd.isnull(extraction_info.iloc[2][14]) else string_formatter(extraction_info.iloc[2][14])
self.sub['lot_elution_buffer'] = extraction_info.iloc[4][14] self.sub['lot_ethanol'] = extraction_info.iloc[3][14] #if pd.isnull(extraction_info.iloc[3][14]) else string_formatter(extraction_info.iloc[3][14])
self.sub['lot_master_mix'] = qprc_info.iloc[0][14] self.sub['lot_elution_buffer'] = extraction_info.iloc[4][14] #if pd.isnull(extraction_info.iloc[4][14]) else string_formatter(extraction_info.iloc[4][14])
self.sub['lot_pre_mix_1'] = qprc_info.iloc[1][14] self.sub['lot_master_mix'] = qprc_info.iloc[0][14] #if pd.isnull(qprc_info.iloc[0][14]) else string_formatter(qprc_info.iloc[0][14])
self.sub['lot_pre_mix_2'] = qprc_info.iloc[2][14] self.sub['lot_pre_mix_1'] = qprc_info.iloc[1][14] #if pd.isnull(qprc_info.iloc[1][14]) else string_formatter(qprc_info.iloc[1][14])
self.sub['lot_positive_control'] = qprc_info.iloc[3][14] self.sub['lot_pre_mix_2'] = qprc_info.iloc[2][14] #if pd.isnull(qprc_info.iloc[2][14]) else string_formatter(qprc_info.iloc[2][14])
self.sub['lot_ddh2o'] = qprc_info.iloc[4][14] self.sub['lot_positive_control'] = qprc_info.iloc[3][14] #if pd.isnull(qprc_info.iloc[3][14]) else string_formatter(qprc_info.iloc[3][14])
self.sub['lot_ddh2o'] = qprc_info.iloc[4][14] #if pd.isnull(qprc_info.iloc[4][14]) else string_formatter(qprc_info.iloc[4][14])
sample_parser = SampleParser(submission_info.iloc[16:40]) sample_parser = SampleParser(submission_info.iloc[16:40])
sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples") sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
self.sub['samples'] = sample_parse() self.sub['samples'] = sample_parse()
@@ -165,3 +168,12 @@ class SampleParser(object):
new_list.append(new) new_list.append(new)
return new_list return new_list
def string_formatter(input):
logger.debug(f"{input} : {type(input)}")
match input:
case int() | float() | np.float64:
return "{:0.0f}".format(input)
case _:
return input

28
src/submissions/configure/__init__.py
View File

@@ -73,15 +73,14 @@ def get_config(settings_path: str|None) -> dict:
Returns: Returns:
setting: dictionary of settings. setting: dictionary of settings.
""" """
# with open("C:\\Users\\lwark\\Desktop\\packagedir.txt", "w") as f:
# f.write(package_dir.__str__())
def join(loader, node): def join(loader, node):
seq = loader.construct_sequence(node) seq = loader.construct_sequence(node)
return ''.join([str(i) for i in seq]) return ''.join([str(i) for i in seq])
## register the tag handler ## register the tag handler
yaml.add_constructor('!join', join) yaml.add_constructor('!join', join)
# if user hasn't defined config path in cli args
logger.debug(f"Making directory: {CONFIGDIR.__str__()}") logger.debug(f"Making directory: {CONFIGDIR.__str__()}")
# make directories
try: try:
CONFIGDIR.mkdir(parents=True) CONFIGDIR.mkdir(parents=True)
except FileExistsError: except FileExistsError:
@@ -91,10 +90,9 @@ def get_config(settings_path: str|None) -> dict:
LOGDIR.mkdir(parents=True) LOGDIR.mkdir(parents=True)
except FileExistsError: except FileExistsError:
pass pass
# if user hasn't defined config path in cli args
if settings_path == None: if settings_path == None:
# Check user .config/ozma directory # Check user .config/submissions directory
# if Path.exists(Path.joinpath(CONFIGDIR, "config.yml")):
# settings_path = Path.joinpath(CONFIGDIR, "config.yml")
if CONFIGDIR.joinpath("config.yml").exists(): if CONFIGDIR.joinpath("config.yml").exists():
settings_path = CONFIGDIR.joinpath("config.yml") settings_path = CONFIGDIR.joinpath("config.yml")
# Check user .ozma directory # Check user .ozma directory
@@ -116,7 +114,6 @@ def get_config(settings_path: str|None) -> dict:
logger.error("No config.yml file found. Using empty dictionary.") logger.error("No config.yml file found. Using empty dictionary.")
return {} return {}
logger.debug(f"Using {settings_path} for config file.") logger.debug(f"Using {settings_path} for config file.")
with open(settings_path, "r") as stream: with open(settings_path, "r") as stream:
try: try:
settings = yaml.load(stream, Loader=yaml.Loader) settings = yaml.load(stream, Loader=yaml.Loader)
@@ -182,22 +179,17 @@ def setup_logger(verbosity:int=3):
# ch = StreamToLogger(logger=logger, log_level=verbosity) # ch = StreamToLogger(logger=logger, log_level=verbosity)
match verbosity: match verbosity:
case 3: case 3:
# verb = logging.DEBUG
ch.setLevel(logging.DEBUG) ch.setLevel(logging.DEBUG)
case 2: case 2:
# verb = logging.INFO
ch.setLevel(logging.INFO) ch.setLevel(logging.INFO)
case 1: case 1:
# verb = logging.WARNING
ch.setLevel(logging.WARNING) ch.setLevel(logging.WARNING)
ch.name = "Stream" ch.name = "Stream"
# create formatter and add it to the handlers # create formatter and add it to the handlers
formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s') formatter = logging.Formatter('%(asctime)s - %(levelname)s - {%(pathname)s:%(lineno)d} - %(message)s')
fh.setFormatter(formatter) fh.setFormatter(formatter)
ch.setFormatter(formatter) ch.setFormatter(formatter)
# ch.setLevel(logging.ERROR)
# add the handlers to the logger # add the handlers to the logger
logger.addHandler(fh) logger.addHandler(fh)
logger.addHandler(ch) logger.addHandler(ch)
def handle_exception(exc_type, exc_value, exc_traceback): def handle_exception(exc_type, exc_value, exc_traceback):
@@ -206,18 +198,10 @@ def setup_logger(verbosity:int=3):
return return
logger.critical("Uncaught exception", exc_info=(exc_type, exc_value, exc_traceback)) logger.critical("Uncaught exception", exc_info=(exc_type, exc_value, exc_traceback))
sys.exit(f"Uncaught error: {exc_type}, {exc_traceback}, check logs.") # sys.exit(f"Uncaught error: {exc_type}, {exc_traceback}, check logs.")
sys.excepthook = handle_exception sys.excepthook = handle_exception
# stderr_logger = logging.getLogger('STDERR')
# sys.stderr = logger
return logger return logger
# sl = StreamToLogger(stderr_logger, logging.ERROR)
# sys.stderr = sl
# def set_logger_verbosity(verbosity): # def set_logger_verbosity(verbosity):
# """Does what it says. # """Does what it says.

14
src/submissions/frontend/__init__.py
View File

@@ -27,7 +27,7 @@ from backend.db import (construct_submission_info, lookup_reagent,
) )
from backend.excel.reports import make_report_xlsx from backend.excel.reports import make_report_xlsx
import numpy import numpy
from frontend.custom_widgets import AddReagentQuestion, AddReagentForm, SubmissionsSheet, ReportDatePicker, KitAdder, ControlsDatePicker from frontend.custom_widgets import AddReagentQuestion, AddReagentForm, SubmissionsSheet, ReportDatePicker, KitAdder, ControlsDatePicker, OverwriteSubQuestion
import logging import logging
import difflib import difflib
@@ -240,9 +240,16 @@ class App(QMainWindow):
parsed_reagents.append(wanted_reagent) parsed_reagents.append(wanted_reagent)
logger.debug(info) logger.debug(info)
info['samples'] = self.samples info['samples'] = self.samples
base_submission = construct_submission_info(ctx=self.ctx, info_dict=info) base_submission, output = construct_submission_info(ctx=self.ctx, info_dict=info)
if output['message'] != None:
dlg = OverwriteSubQuestion(output['message'], base_submission.rsl_plate_num)
if dlg.exec():
base_submission.reagents = []
else:
return
for reagent in parsed_reagents: for reagent in parsed_reagents:
base_submission.reagents.append(reagent) base_submission.reagents.append(reagent)
logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
result = store_submission(ctx=self.ctx, base_submission=base_submission) result = store_submission(ctx=self.ctx, base_submission=base_submission)
if result != None: if result != None:
msg = QMessageBox() msg = QMessageBox()
@@ -250,8 +257,11 @@ class App(QMainWindow):
msg.setText("Error") msg.setText("Error")
msg.setInformativeText(result['message']) msg.setInformativeText(result['message'])
msg.setWindowTitle("Error") msg.setWindowTitle("Error")
msg.show()
msg.exec() msg.exec()
self.table_widget.sub_wid.setData() self.table_widget.sub_wid.setData()
for item in self.table_widget.formlayout.parentWidget().findChildren(QWidget):
item.setParent(None)
def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None): def add_reagent(self, reagent_lot:str|None=None, reagent_type:str|None=None):

19
src/submissions/frontend/custom_widgets/__init__.py
View File

@@ -44,6 +44,25 @@ class AddReagentQuestion(QDialog):
self.setLayout(self.layout) self.setLayout(self.layout)
class OverwriteSubQuestion(QDialog):
def __init__(self, message:str, rsl_plate_num:str):
super().__init__()
self.setWindowTitle(f"Overwrite {rsl_plate_num}?")
QBtn = QDialogButtonBox.StandardButton.Yes | QDialogButtonBox.StandardButton.No
self.buttonBox = QDialogButtonBox(QBtn)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
self.layout = QVBoxLayout()
message = QLabel(message)
self.layout.addWidget(message)
self.layout.addWidget(self.buttonBox)
self.setLayout(self.layout)
class AddReagentForm(QDialog): class AddReagentForm(QDialog):
def __init__(self, ctx:dict, reagent_lot:str|None, reagent_type:str|None): def __init__(self, ctx:dict, reagent_lot:str|None, reagent_type:str|None):
super().__init__() super().__init__()