Code cleanup, dependency update, various bug fixes
This commit is contained in:
lwark
@@ -107,6 +107,12 @@ class BasicSubmission(BaseClass):
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@classmethod
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def jsons(cls) -> List[str]:
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"""
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Get list of JSON db columns
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Returns:
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List[str]: List of column names
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"""
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output = [item.name for item in cls.__table__.columns if isinstance(item.type, JSON)]
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if issubclass(cls, BasicSubmission) and not cls.__name__ == "BasicSubmission":
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output += BasicSubmission.jsons()
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@@ -114,6 +120,12 @@ class BasicSubmission(BaseClass):
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@classmethod
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def timestamps(cls) -> List[str]:
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"""
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Get list of TIMESTAMP columns
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Returns:
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List[str]: List of column names
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"""
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output = [item.name for item in cls.__table__.columns if isinstance(item.type, TIMESTAMP)]
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if issubclass(cls, BasicSubmission) and not cls.__name__ == "BasicSubmission":
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output += BasicSubmission.timestamps()
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@@ -122,7 +134,7 @@ class BasicSubmission(BaseClass):
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# TODO: Beef up this to include info_map from DB
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@classmethod
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def get_default_info(cls, *args):
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# Create defaults for all submission_types
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# NOTE: Create defaults for all submission_types
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parent_defs = super().get_default_info()
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recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
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dicto = dict(
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@@ -132,9 +144,7 @@ class BasicSubmission(BaseClass):
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# NOTE: Fields not placed in ui form
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form_ignore=['reagents', 'ctx', 'id', 'cost', 'extraction_info', 'signed_by', 'comment'] + recover,
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# NOTE: Fields not placed in ui form to be moved to pydantic
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form_recover=recover,
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# parser_ignore=['samples', 'signed_by'] + [item for item in cls.jsons() if item != "comment"],
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# excel_ignore=[],
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form_recover=recover
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)
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# logger.debug(dicto['singles'])
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# NOTE: Singles tells the query which fields to set limit to 1
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@@ -151,7 +161,6 @@ class BasicSubmission(BaseClass):
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st = cls.get_submission_type()
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if st is None:
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logger.error("No default info for BasicSubmission.")
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# return output
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else:
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output['submission_type'] = st.name
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for k, v in st.defaults.items():
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@@ -169,16 +178,37 @@ class BasicSubmission(BaseClass):
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return output
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@classmethod
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def get_submission_type(cls):
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def get_submission_type(cls) -> SubmissionType:
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"""
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Gets the SubmissionType associated with this class
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Returns:
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SubmissionType: SubmissionType with name equal to this polymorphic identity
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"""
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name = cls.__mapper_args__['polymorphic_identity']
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return SubmissionType.query(name=name)
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@classmethod
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def construct_info_map(cls, mode:Literal['read', 'write']):
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def construct_info_map(cls, mode:Literal["read", "write"]) -> dict:
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"""
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Method to call submission type's construct info map.
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Args:
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mode (Literal["read", "write"]): Which map to construct.
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Returns:
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dict: Map of info locations.
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"""
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return cls.get_submission_type().construct_info_map(mode=mode)
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@classmethod
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def construct_sample_map(cls):
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def construct_sample_map(cls) -> dict:
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"""
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Method to call submission type's construct_sample_map
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Returns:
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dict: sample location map
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"""
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return cls.get_submission_type().construct_sample_map()
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def to_dict(self, full_data: bool = False, backup: bool = False, report: bool = False) -> dict:
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@@ -192,7 +222,7 @@ class BasicSubmission(BaseClass):
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Returns:
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dict: dictionary used in submissions summary and details
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"""
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# get lab from nested organization object
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# NOTE: get lab from nested organization object
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# logger.debug(f"Converting {self.rsl_plate_num} to dict...")
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try:
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sub_lab = self.submitting_lab.name
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@@ -202,12 +232,12 @@ class BasicSubmission(BaseClass):
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sub_lab = sub_lab.replace("_", " ").title()
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except AttributeError:
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pass
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# get extraction kit name from nested kit object
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# NOTE: get extraction kit name from nested kit object
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try:
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ext_kit = self.extraction_kit.name
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except AttributeError:
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ext_kit = None
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# load scraped extraction info
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# NOTE: load scraped extraction info
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try:
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ext_info = self.extraction_info
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except TypeError:
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@@ -324,7 +354,7 @@ class BasicSubmission(BaseClass):
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def make_plate_map(self, plate_rows: int = 8, plate_columns=12) -> str:
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"""
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Constructs an html based plate map.
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Constructs an html based plate map for submission details.
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Args:
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sample_list (list): List of submission samples
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@@ -386,7 +416,7 @@ class BasicSubmission(BaseClass):
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subs = [item.to_dict() for item in cls.query(submission_type=submission_type, limit=limit, chronologic=chronologic)]
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# logger.debug(f"Got {len(subs)} submissions.")
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df = pd.DataFrame.from_records(subs)
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# Exclude sub information
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# NOTE: Exclude sub information
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for item in ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents',
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'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls']:
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try:
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@@ -414,9 +444,6 @@ class BasicSubmission(BaseClass):
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# logger.debug(f"Looking up organization: {value}")
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field_value = Organization.query(name=value)
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# logger.debug(f"Got {field_value} for organization {value}")
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# case "submitter_plate_num":
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# # logger.debug(f"Submitter plate id: {value}")
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# field_value = value
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case "samples":
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for sample in value:
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# logger.debug(f"Parsing {sample} to sql.")
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@@ -436,17 +463,6 @@ class BasicSubmission(BaseClass):
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field_value = value
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case "ctx" | "csv" | "filepath" | "equipment":
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return
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# case "comment":
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# if value == "" or value == None or value == 'null':
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# field_value = None
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# else:
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# field_value = dict(name=getuser(), text=value, time=datetime.now())
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# # if self.comment is None:
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# # self.comment = [field_value]
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# # else:
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# # self.comment.append(field_value)
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# self.update_json(field=key, value=field_value)
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# return
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case item if item in self.jsons():
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logger.debug(f"Setting JSON attribute.")
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existing = self.__getattribute__(key)
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@@ -1852,13 +1868,6 @@ class WastewaterArtic(BasicSubmission):
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set_plate = None
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for assoc in self.submission_sample_associations:
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dicto = assoc.to_sub_dict()
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# old_sub = assoc.sample.get_previous_ww_submission(current_artic_submission=self)
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# try:
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# dicto['plate_name'] = old_sub.rsl_plate_num
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# except AttributeError:
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# dicto['plate_name'] = ""
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# old_assoc = WastewaterAssociation.query(submission=old_sub, sample=assoc.sample, limit=1)
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# dicto['well'] = f"{row_map[old_assoc.row]}{old_assoc.column}"
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for item in self.source_plates:
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old_plate = WastewaterAssociation.query(submission=item['plate'], sample=assoc.sample, limit=1)
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if old_plate is not None:
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@@ -1879,6 +1888,12 @@ class WastewaterArtic(BasicSubmission):
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events['Gel Box'] = self.gel_box
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return events
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def set_attribute(self, key: str, value):
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super().set_attribute(key=key, value=value)
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if key == 'gel_info':
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if len(self.gel_info) > 3:
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self.gel_info = self.gel_info[-3:]
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def gel_box(self, obj):
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"""
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Creates widget to perform gel viewing operations
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