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Moments before disaster.

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This commit is contained in:
lwark
2024-10-09 12:44:06 -05:00
parent ae5fb1b48f
commit 066d1af0f2
5 changed files with 101 additions and 6 deletions
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2
src/submissions/backend/db/models/controls.py
View File

@@ -84,7 +84,7 @@ class ControlType(BaseClass):
Returns:
List[ControlType]: Control types that have targets
"""
return [item for item in cls.query() if item.targets]
return (item for item in cls.query() if item.targets)
@classmethod
def build_positive_regex(cls) -> Pattern:

23
src/submissions/backend/db/models/submissions.py
View File

@@ -506,7 +506,7 @@ class BasicSubmission(BaseClass):
Returns:
List[str]: List of names
"""
return [item.role for item in self.submission_equipment_associations]
return (item.role for item in self.submission_equipment_associations)
@classmethod
def submissions_to_df(cls, submission_type: str | None = None, limit: int = 0,
@@ -527,7 +527,8 @@ 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, page=page, page_size=page_size)]
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}")
@@ -971,6 +972,19 @@ class BasicSubmission(BaseClass):
# samples.append(sample)
# return samples
@classmethod
def parse_pcr_controls(cls, xl: Workbook) -> list:
location_map = cls.get_submission_type().sample_map['pcr_controls']
name_column = 1
for item in location_map:
logger.debug(f"Looking for {item['name']}")
worksheet = xl[item['sheet']]
for iii, row in enumerate(worksheet.iter_rows(max_row=len(worksheet['A']), max_col=name_column), start=1):
for cell in row:
if cell.value == item['name']:
logger.debug(f"Pulling from row {iii}, column {item['ct_column']}")
yield dict(name=item['name'], ct=worksheet.cell(row=iii, column=item['ct_column']).value)
@classmethod
def filename_template(cls) -> str:
"""
@@ -1560,6 +1574,11 @@ class Wastewater(BasicSubmission):
for sample in output:
yield sample
# @classmethod
# def parse_pcr_controls(cls, xl: Workbook, location_map: list) -> list:
@classmethod
def enforce_name(cls, instr: str, data: dict | None = {}) -> str:
"""

74
src/submissions/backend/excel/parser.py
View File

@@ -1,6 +1,7 @@
'''
contains parser objects for pulling values from client generated submission sheets.
'''
import json
from copy import copy
from getpass import getuser
from pprint import pformat
@@ -142,7 +143,6 @@ class SheetParser(object):
return PydSubmission(filepath=self.filepath, run_custom=True, **self.sub)
class InfoParser(object):
"""
Object to parse generic info from excel sheet.
@@ -675,6 +675,7 @@ class PCRParser(object):
rsl_plate_num = self.submission_obj.rsl_plate_num
self.pcr = self.parse_general()
self.samples = self.submission_obj.parse_pcr(xl=self.xl, rsl_plate_num=rsl_plate_num)
self.controls = self.submission_obj.parse_pcr_controls(xl=self.xl)
def parse_general(self):
"""
@@ -698,3 +699,74 @@ class PCRParser(object):
pcr['imported_by'] = getuser()
# logger.debug(f"PCR: {pformat(pcr)}")
return pcr
class EDSParser(object):
expand_device = {"QS7PRO": "QuantStudio tm 7 Pro System"}
expand_block = {"BLOCK_96W_01ML": "96-Well 0.1-mL Block"}
def __init__(self, filepath: str | Path | None = None):
logger.info(f"\n\nParsing {filepath.__str__()}\n\n")
match filepath:
case Path():
self.filepath = filepath
case str():
self.filepath = Path(filepath)
case _:
logger.error(f"No filepath given.")
raise ValueError("No filepath given.")
self.eds = ZipFile(self.filepath)
self.analysis_settings = json.loads(self.eds.read("primary/analysis_setting.json").decode("utf-8"))
self.analysis_results = json.loads(self.eds.read("primary/analysis_setting.json").decode("utf-8"))
self.presence_absence_results = json.loads(
self.eds.read("extensions/am.pa/presence_absence_result.json").decode("utf-8"))
self.presence_absence_settings = json.loads(
self.eds.read("extensions/am.pa/presence_absence_setting.json").decode("utf-8"))
self.run_summary = json.loads(self.eds.read("run/run_summary.json").decode("utf-8"))
self.run_method = json.loads(self.eds.read("setup/run_method.json").decode("utf-8"))
self.plate_setup = json.loads(self.eds.read("setup/plate_setup.json").decode("utf-8"))
self.eds_summary = json.loads(self.eds.read("summary.json").decode("utf-8"))
def parse_DA_date_format(self, value: int) -> datetime:
value = value / 1000
return datetime.utcfromtimestamp(value)
def get_run_time(self, start: datetime, end: datetime) -> Tuple[str, str, str]:
delta = end - start
minutes, seconds = divmod(delta.seconds, 60)
duration = f"{minutes} minutes {seconds} seconds"
start_time = start.strftime("%Y-%m-%d %I:%M:%S %p %Z")
end_time = end.strftime("%Y-%m-%d %I:%M:%S %p %Z")
return start_time, end_time, duration
def parse_summary(self):
summary = dict()
summary['file_name'] = self.filepath.absolute().__str__()
summary['comment'] = self.eds_summary['description']
summary['operator'] = self.run_summary['operator']
summary['barcode'] = self.plate_setup['plateBarcode']
try:
summary['instrument_type'] = self.__class__.expand_device[self.eds_summary['instrumentType']]
except KeyError:
summary['instrument_type'] = self.eds_summary['instrumentType']
try:
summary['block_type'] = self.__class__.expand_block[self.plate_setup['blockType']]
except KeyError:
summary['block_type'] = self.plate_setup['blockType']
summary['instrument_name'] = self.run_summary['instrumentName']
summary['instrument_serial_number'] = self.run_summary['instrumentSerialNumber']
summary['heated_cover_serial_number'] = self.run_summary['coverSerialNumber']
summary['block_serial_number'] = self.run_summary['blockSerialNumber']
run_start = self.parse_DA_date_format(self.run_summary['startTime'])
run_end = self.parse_DA_date_format(self.run_summary['endTime'])
summary['run_start_date/time'], summary['run_end_date/time'], summary['run_duration'] = \
self.get_run_time(run_start, run_end)
summary['sample_volume'] = self.run_method['sampleVolume']
summary['cover_temperature'] = self.run_method['coverTemperature']
summary['passive_reference'] = self.plate_setup['passiveReference']
summary['pcr_stage/step_number'] = f"Stage {self.analysis_settings['cqAnalysisStageNumber']} Step {self.analysis_settings['cqAnalysisStepNumber']}"
summary['quantification_cycle_method'] = self.analysis_results['cqAlgorithmType']
summary['analysis_date/time'] = self.parse_DA_date_format(self.eds_summary['analysis']['primary']['analysisTime'])
summary['software_name_and_version'] = "Design & Analysis Software v2.8.0"
summary['plugin_name_and_version'] = "Primary Analysis v1.8.1, Presence Absence v2.4.0"
return summary