Replaced some list comprehension with generators, javascript in templates to create click event.
This commit is contained in:
lwark
@@ -53,7 +53,6 @@ class SheetParser(object):
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self.parse_samples()
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self.parse_equipment()
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self.parse_tips()
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# self.finalize_parse()
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# logger.debug(f"Parser.sub after info scrape: {pformat(self.sub)}")
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def parse_info(self):
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@@ -63,6 +62,8 @@ class SheetParser(object):
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parser = InfoParser(xl=self.xl, submission_type=self.submission_type, sub_object=self.sub_object)
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info = parser.parse_info()
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self.info_map = parser.map
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# NOTE: in order to accommodate generic submission types we have to check for the type in the excel sheet and
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# rerun accordingly
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try:
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check = info['submission_type']['value'] not in [None, "None", "", " "]
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except KeyError:
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@@ -78,13 +79,15 @@ class SheetParser(object):
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else:
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self.submission_type = RSLNamer.retrieve_submission_type(filename=self.filepath)
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self.parse_info()
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for k, v in info.items():
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match k:
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# NOTE: exclude samples.
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case "sample":
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continue
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case _:
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self.sub[k] = v
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[self.sub.__setitem__(k, v) for k, v in info.items()]
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# for k, v in info.items():
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# match k:
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# # NOTE: exclude samples.
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# case "sample":
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# logger.debug(f"Sample found: {k}: {v}")
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# continue
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# case _:
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# self.sub[k] = v
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def parse_reagents(self, extraction_kit: str | None = None):
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"""
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@@ -105,7 +108,7 @@ class SheetParser(object):
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Calls sample parser to pull info from the excel sheet
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"""
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parser = SampleParser(xl=self.xl, submission_type=self.submission_type)
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self.sub['samples'] = parser.reconcile_samples()
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self.sub['samples'] = parser.parse_samples()
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def parse_equipment(self):
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"""
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@@ -145,29 +148,29 @@ class SheetParser(object):
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PydSubmission: output pydantic model
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"""
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# logger.debug(f"Submission dictionary coming into 'to_pydantic':\n{pformat(self.sub)}")
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pyd_dict = copy(self.sub)
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pyd_dict['samples'] = [PydSample(**sample) for sample in self.sub['samples']]
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# pyd_dict = copy(self.sub)
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# self.sub['samples'] = [PydSample(**sample) for sample in self.sub['samples']]
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# logger.debug(f"Reagents: {pformat(self.sub['reagents'])}")
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pyd_dict['reagents'] = [PydReagent(**reagent) for reagent in self.sub['reagents']]
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# self.sub['reagents'] = [PydReagent(**reagent) for reagent in self.sub['reagents']]
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# logger.debug(f"Equipment: {self.sub['equipment']}")
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try:
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check = bool(self.sub['equipment'])
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except TypeError:
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check = False
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if check:
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pyd_dict['equipment'] = [PydEquipment(**equipment) for equipment in self.sub['equipment']]
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else:
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pyd_dict['equipment'] = None
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try:
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check = bool(self.sub['tips'])
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except TypeError:
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check = False
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if check:
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pyd_dict['tips'] = [PydTips(**tips) for tips in self.sub['tips']]
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else:
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pyd_dict['tips'] = None
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psm = PydSubmission(filepath=self.filepath, run_custom=True, **pyd_dict)
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return psm
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# try:
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# check = bool(self.sub['equipment'])
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# except TypeError:
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# check = False
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# if check:
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# self.sub['equipment'] = [PydEquipment(**equipment) for equipment in self.sub['equipment']]
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# else:
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# self.sub['equipment'] = None
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# try:
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# check = bool(self.sub['tips'])
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# except TypeError:
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# check = False
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# if check:
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# self.sub['tips'] = [PydTips(**tips) for tips in self.sub['tips']]
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# else:
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# self.sub['tips'] = None
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return PydSubmission(filepath=self.filepath, run_custom=True, **self.sub)
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# return psm
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class InfoParser(object):
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@@ -287,7 +290,7 @@ class ReagentParser(object):
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extraction_kit (str): Extraction kit used.
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sub_object (BasicSubmission | None, optional): Submission object holding methods. Defaults to None.
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"""
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# logger.debug("\n\nHello from ReagentParser!\n\n")
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logger.debug("\n\nHello from ReagentParser!\n\n")
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if isinstance(submission_type, str):
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submission_type = SubmissionType.query(name=submission_type)
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self.submission_type_obj = submission_type
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@@ -382,7 +385,7 @@ class SampleParser(object):
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sample_map (dict | None, optional): Locations in database where samples are found. Defaults to None.
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sub_object (BasicSubmission | None, optional): Submission object holding methods. Defaults to None.
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"""
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# logger.debug("\n\nHello from SampleParser!\n\n")
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logger.debug("\n\nHello from SampleParser!\n\n")
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self.samples = []
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self.xl = xl
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if isinstance(submission_type, str):
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@@ -477,49 +480,50 @@ class SampleParser(object):
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lookup_samples.append(self.samp_object.parse_sample(row_dict))
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return lookup_samples
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def parse_samples(self) -> Tuple[Report | None, List[dict] | List[PydSample]]:
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"""
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Parse merged platemap/lookup info into dicts/samples
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# def parse_samples(self) -> Tuple[Report | None, List[dict] | List[PydSample]]:
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# """
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# Parse merged platemap/lookup info into dicts/samples
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#
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# Returns:
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# List[dict]|List[models.BasicSample]: List of samples
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# """
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# result = None
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# new_samples = []
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# # logger.debug(f"Starting samples: {pformat(self.samples)}")
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# for sample in self.samples:
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# translated_dict = {}
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# for k, v in sample.items():
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# match v:
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# case dict():
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# v = None
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# case float():
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# v = convert_nans_to_nones(v)
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# case _:
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# v = v
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# translated_dict[k] = convert_nans_to_nones(v)
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# translated_dict['sample_type'] = f"{self.submission_type} Sample"
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# translated_dict = self.sub_object.parse_samples(translated_dict)
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# translated_dict = self.samp_object.parse_sample(translated_dict)
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# # logger.debug(f"Here is the output of the custom parser:\n{translated_dict}")
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# new_samples.append(PydSample(**translated_dict))
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# return result, new_samples
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Returns:
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List[dict]|List[models.BasicSample]: List of samples
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"""
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result = None
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new_samples = []
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# logger.debug(f"Starting samples: {pformat(self.samples)}")
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for sample in self.samples:
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translated_dict = {}
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for k, v in sample.items():
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match v:
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case dict():
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v = None
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case float():
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v = convert_nans_to_nones(v)
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case _:
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v = v
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translated_dict[k] = convert_nans_to_nones(v)
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translated_dict['sample_type'] = f"{self.submission_type} Sample"
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translated_dict = self.sub_object.parse_samples(translated_dict)
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translated_dict = self.samp_object.parse_sample(translated_dict)
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# logger.debug(f"Here is the output of the custom parser:\n{translated_dict}")
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new_samples.append(PydSample(**translated_dict))
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return result, new_samples
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def reconcile_samples(self) -> Generator[dict, None, None]:
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def parse_samples(self) -> Generator[dict, None, None]:
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"""
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Merges sample info from lookup table and plate map.
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Returns:
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List[dict]: Reconciled samples
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"""
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if self.plate_map_samples is None or self.lookup_samples is None:
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if not self.plate_map_samples or not self.lookup_samples:
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logger.error(f"No separate samples, returning")
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self.samples = self.lookup_samples or self.plate_map_samples
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return
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merge_on_id = self.sample_info_map['lookup_table']['merge_on_id']
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plate_map_samples = sorted(copy(self.plate_map_samples), key=lambda d: d['id'])
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lookup_samples = sorted(copy(self.lookup_samples), key=lambda d: d[merge_on_id])
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print(pformat(plate_map_samples))
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print(pformat(lookup_samples))
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# print(pformat(plate_map_samples))
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# print(pformat(lookup_samples))
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for ii, psample in enumerate(plate_map_samples):
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try:
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check = psample['id'] == lookup_samples[ii][merge_on_id]
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@@ -563,6 +567,7 @@ class EquipmentParser(object):
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xl (Workbook): Openpyxl workbook from submitted excel file.
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submission_type (str | SubmissionType): Type of submission expected (Wastewater, Bacterial Culture, etc.)
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"""
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logger.debug("\n\nHello from EquipmentParser!\n\n")
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if isinstance(submission_type, str):
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submission_type = SubmissionType.query(name=submission_type)
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self.submission_type = submission_type
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@@ -649,6 +654,7 @@ class TipParser(object):
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xl (Workbook): Openpyxl workbook from submitted excel file.
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submission_type (str | SubmissionType): Type of submission expected (Wastewater, Bacterial Culture, etc.)
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"""
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logger.debug("\n\nHello from TipParser!\n\n")
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if isinstance(submission_type, str):
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submission_type = SubmissionType.query(name=submission_type)
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self.submission_type = submission_type
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