Pre code clean-up
This commit is contained in:
lwark
@@ -260,7 +260,7 @@ 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.info("\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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@@ -303,11 +303,11 @@ class ReagentParser(object):
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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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@@ -325,10 +325,10 @@ class ReagentParser(object):
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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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@@ -353,12 +353,12 @@ 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.info("\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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submission_type = SubmissionType.query(name=submission_type)
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logger.debug(f"Sample parser is using submission type: {submission_type}")
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# logger.debug(f"Sample parser is using submission type: {submission_type}")
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self.submission_type = submission_type.name
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self.submission_type_obj = submission_type
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if sub_object is None:
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@@ -456,40 +456,49 @@ class SampleParser(object):
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List[dict]: Reconciled samples
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"""
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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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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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check = False
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if check:
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# logger.debug(f"Direct match found for {psample['id']}")
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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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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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except KeyError:
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check = False
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if check:
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new = lsample | psample
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lookup_samples[jj] = {}
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break
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else:
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new = psample
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if not check_key_or_attr(key='submitter_id', interest=new, check_none=True):
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new['submitter_id'] = psample['id']
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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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logger.warning(f"No separate samples")
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samples = self.lookup_samples or self.plate_map_samples
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for new in samples:
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if not check_key_or_attr(key='submitter_id', interest=new, check_none=True):
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new['submitter_id'] = new['id']
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new = self.sub_object.parse_samples(new)
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try:
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del new['id']
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except KeyError:
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pass
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yield new
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else:
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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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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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check = False
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if check:
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# logger.debug(f"Direct match found for {psample['id']}")
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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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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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except KeyError:
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check = False
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if check:
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new = lsample | psample
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lookup_samples[jj] = {}
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break
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else:
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new = psample
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if not check_key_or_attr(key='submitter_id', interest=new, check_none=True):
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new['submitter_id'] = psample['id']
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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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class EquipmentParser(object):
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