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Added report tab with HTML and excel export.

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This commit is contained in:
lwark
2024-10-04 15:24:00 -05:00
parent c89ec2b62c
commit 5fe5c22222
5 changed files with 106 additions and 88 deletions
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41
src/submissions/backend/db/models/submissions.py
View File

@@ -13,7 +13,7 @@ from tempfile import TemporaryDirectory, TemporaryFile
from operator import itemgetter
from pprint import pformat
from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, desc
from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.orm.attributes import flag_modified
from sqlalchemy.ext.associationproxy import association_proxy
@@ -283,7 +283,7 @@ class BasicSubmission(BaseClass):
del input_dict['id']
return input_dict
def generate_associations(self, name:str, extra:str|None=None):
def generate_associations(self, name: str, extra: str | None = None):
try:
field = self.__getattribute__(name)
except AttributeError:
@@ -479,15 +479,6 @@ class BasicSubmission(BaseClass):
Returns:
str: html output string.
"""
# output_samples = []
# logger.debug("Setting locations.")
# for column in range(1, plate_columns + 1):
# for row in range(1, plate_rows + 1):
# try:
# well = next((item for item in sample_list if item['row'] == row and item['column'] == column), dict(name="", row=row, column=column, background_color="#ffffff"))
# except StopIteration:
# well = dict(name="", row=row, column=column, background_color="#ffffff")
# output_samples.append(well)
rows = range(1, plate_rows + 1)
columns = range(1, plate_columns + 1)
# NOTE: An overly complicated list comprehension create a list of sample locations
@@ -512,11 +503,12 @@ class BasicSubmission(BaseClass):
@classmethod
def submissions_to_df(cls, submission_type: str | None = None, limit: int = 0,
chronologic: bool = True) -> pd.DataFrame:
chronologic: bool = True, page: int = 1, page_size: int = 250) -> pd.DataFrame:
"""
Convert all submissions to dataframe
Args:
page (int, optional): Limits the number of submissions to a page size. Defaults to 1.
chronologic (bool, optional): Sort submissions in chronologic order. Defaults to True.
submission_type (str | None, optional): Filter by SubmissionType. Defaults to None.
limit (int, optional): Maximum number of results to return. Defaults to 0.
@@ -528,16 +520,16 @@ class BasicSubmission(BaseClass):
# logger.debug(f"Using limit: {limit}")
# NOTE: use lookup function to create list of dicts
subs = [item.to_dict() for item in
cls.query(submission_type=submission_type, limit=limit, chronologic=chronologic)]
cls.query(submission_type=submission_type, limit=limit, chronologic=chronologic, page=page, page_size=page_size)]
# logger.debug(f"Got {len(subs)} submissions.")
df = pd.DataFrame.from_records(subs)
# logger.debug(f"Column names: {df.columns}")
# NOTE: Exclude sub information
exclude = ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents',
'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls',
'source_plates', 'pcr_technician', 'ext_technician', 'artic_technician', 'cost_centre',
'signed_by', 'artic_date', 'gel_barcode', 'gel_date', 'ngs_date', 'contact_phone', 'contact',
'tips', 'gel_image_path', 'custom']
'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls',
'source_plates', 'pcr_technician', 'ext_technician', 'artic_technician', 'cost_centre',
'signed_by', 'artic_date', 'gel_barcode', 'gel_date', 'ngs_date', 'contact_phone', 'contact',
'tips', 'gel_image_path', 'custom']
df = df.loc[:, ~df.columns.isin(exclude)]
# for item in excluded:
# try:
@@ -829,7 +821,7 @@ class BasicSubmission(BaseClass):
return input_dict
@classmethod
def custom_validation(cls, pyd:"PydSubmission") -> dict:
def custom_validation(cls, pyd: "PydSubmission") -> dict:
"""
Performs any final custom parsing of the excel file.
@@ -886,7 +878,6 @@ class BasicSubmission(BaseClass):
ws.cell(row=item['row'], column=item['column'], value=item['value'])
return input_excel
@classmethod
def enforce_name(cls, instr: str, data: dict | None = {}) -> str:
"""
@@ -1061,6 +1052,8 @@ class BasicSubmission(BaseClass):
reagent: Reagent | str | None = None,
chronologic: bool = False,
limit: int = 0,
page: int = 1,
page_size: int = 250,
**kwargs
) -> BasicSubmission | List[BasicSubmission]:
"""
@@ -1161,7 +1154,13 @@ class BasicSubmission(BaseClass):
case _:
pass
if chronologic:
query.order_by(cls.submitted_date)
logger.debug("Attempting sort by date descending")
query = query.order_by(cls.submitted_date.desc())
if page_size is not None:
query = query.limit(page_size)
page = page - 1
if page is not None:
query = query.offset(page * page_size)
return cls.execute_query(query=query, model=model, limit=limit, **kwargs)
@classmethod
@@ -2483,7 +2482,7 @@ class BasicSample(BaseClass):
df = pd.DataFrame.from_records(samples)
# NOTE: Exclude sub information
exclude = ['concentration', 'organism', 'colour', 'tooltip', 'comments', 'samples', 'reagents',
'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls']
'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls']
df = df.loc[:, ~df.columns.isin(exclude)]
return df

2
src/submissions/backend/validators/pydant.py
View File

@@ -611,7 +611,7 @@ class PydSubmission(BaseModel, extra='allow'):
@classmethod
def expand_samples(cls, value):
if isinstance(value, Generator):
# logger.debug("We have a generator")
# logger.debug("We have a generator")[
return [PydSample(**sample) for sample in value]
return value