Increasing generator usage.
This commit is contained in:
lwark
@@ -80,14 +80,6 @@ class SheetParser(object):
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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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[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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@@ -147,30 +139,8 @@ class SheetParser(object):
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Returns:
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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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# 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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# 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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# 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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@@ -298,6 +268,7 @@ class ReagentParser(object):
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if isinstance(extraction_kit, dict):
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extraction_kit = extraction_kit['value']
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self.kit_object = KitType.query(name=extraction_kit)
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# logger.debug(f"Got extraction kit object: {self.kit_object}")
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self.map = self.fetch_kit_info_map(submission_type=submission_type)
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# logger.debug(f"Reagent Parser map: {self.map}")
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self.xl = xl
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@@ -329,15 +300,14 @@ class ReagentParser(object):
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Returns:
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List[PydReagent]: List of parsed reagents.
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"""
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# listo = []
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for sheet in self.xl.sheetnames:
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ws = self.xl[sheet]
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relevant = {k.strip(): v for k, v in self.map.items() if sheet in self.map[k]['sheet']}
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# logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
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logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
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if relevant == {}:
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continue
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for item in relevant:
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# logger.debug(f"Attempting to scrape: {item}")
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logger.debug(f"Attempting to scrape: {item}")
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try:
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reagent = relevant[item]
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name = ws.cell(row=reagent['name']['row'], column=reagent['name']['column']).value
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@@ -350,16 +320,15 @@ class ReagentParser(object):
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comment = ""
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except (KeyError, IndexError):
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yield dict(role=item.strip(), lot=None, expiry=None, name=None, comment="", missing=True)
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# continue
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# NOTE: If the cell is blank tell the PydReagent
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if check_not_nan(lot):
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missing = False
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else:
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missing = True
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# logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}")
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logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}")
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lot = str(lot)
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# logger.debug(
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# f"Going into pydantic: name: {name}, lot: {lot}, expiry: {expiry}, type: {item.strip()}, comment: {comment}")
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logger.debug(
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f"Going into pydantic: name: {name}, lot: {lot}, expiry: {expiry}, type: {item.strip()}, comment: {comment}")
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try:
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check = name.lower() != "not applicable"
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except AttributeError:
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@@ -368,7 +337,6 @@ class ReagentParser(object):
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if check:
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yield dict(role=item.strip(), lot=lot, expiry=expiry, name=name, comment=comment,
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missing=missing)
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# return listo
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class SampleParser(object):
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@@ -480,34 +448,6 @@ 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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#
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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 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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@@ -522,9 +462,8 @@ class SampleParser(object):
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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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for ii, psample in enumerate(plate_map_samples):
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# NOTE: See if we can do this the easy way and just use the same list index.
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try:
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check = psample['id'] == lookup_samples[ii][merge_on_id]
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except (KeyError, IndexError):
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@@ -534,7 +473,7 @@ class SampleParser(object):
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new = lookup_samples[ii] | psample
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lookup_samples[ii] = {}
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else:
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# logger.warning(f"Match for {psample['id']} not direct, running search.")
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logger.warning(f"Match for {psample['id']} not direct, running search.")
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for jj, lsample in enumerate(lookup_samples):
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try:
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check = lsample[merge_on_id] == psample['id']
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@@ -551,9 +490,6 @@ class SampleParser(object):
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new = self.sub_object.parse_samples(new)
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del new['id']
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yield new
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# samples.append(new)
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# samples = remove_key_from_list_of_dicts(samples, "id")
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# return sorted(samples, key=lambda k: (k['row'], k['column']))
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class EquipmentParser(object):
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