Ui interface updates.
This commit is contained in:
lwark
@@ -13,6 +13,7 @@ from sqlalchemy import Column, INTEGER, String, JSON
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from sqlalchemy.ext.associationproxy import AssociationProxy
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from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session, InstrumentedAttribute, ColumnProperty
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from sqlalchemy.ext.declarative import declared_attr
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from sqlalchemy.ext.hybrid import hybrid_property
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from sqlalchemy.exc import ArgumentError
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from typing import Any, List, ClassVar
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from pathlib import Path
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@@ -237,10 +238,10 @@ class BaseClass(Base):
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@classmethod
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def query_or_create(cls, **kwargs) -> Tuple[Any, bool]:
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new = False
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allowed = [k for k, v in cls.__dict__.items() if isinstance(v, InstrumentedAttribute)]
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allowed = [k for k, v in cls.__dict__.items() if isinstance(v, InstrumentedAttribute) or isinstance(v, hybrid_property)]
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# and not isinstance(v.property, _RelationshipDeclared)]
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sanitized_kwargs = {k: v for k, v in kwargs.items() if k in allowed}
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# logger.debug(f"Sanitized kwargs: {sanitized_kwargs}")
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logger.debug(f"Sanitized kwargs: {sanitized_kwargs}")
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instance = cls.query(**sanitized_kwargs)
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if not instance or isinstance(instance, list):
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instance = cls()
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@@ -273,7 +274,7 @@ class BaseClass(Base):
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return cls.execute_query(**kwargs)
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@classmethod
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def execute_query(cls, query: Query = None, model=None, limit: int = 0, **kwargs) -> Any | List[Any]:
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def execute_query(cls, query: Query = None, model=None, limit: int = 0, offset:int|None=None, **kwargs) -> Any | List[Any]:
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"""
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Execute sqlalchemy query with relevant defaults.
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@@ -291,22 +292,32 @@ class BaseClass(Base):
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# logger.debug(f"Model: {model}")
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if query is None:
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query: Query = cls.__database_session__.query(cls)
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else:
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logger.debug(f"Incoming query: {query}")
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singles = cls.get_default_info('singles')
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for k, v in kwargs.items():
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logger.info(f"Using key: {k} with value: {v}")
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logger.info(f"Using key: {k} with value: {v} against {cls}")
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try:
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attr = getattr(cls, k)
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# NOTE: account for attrs that use list.
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if attr.property.uselist:
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query = query.filter(attr.contains(v))
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else:
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query = query.filter(attr == v)
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except (ArgumentError, AttributeError) as e:
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logger.error(f"Attribute {k} unavailable due to:\n\t{e}\nSkipping.")
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logger.error(f"Attribute {k} unavailable due to:\n\t{e}\n.")
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continue
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# NOTE: account for attrs that use list.
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try:
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check = attr.property.uselist
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except AttributeError:
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check = False
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if check:
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logger.debug("Got uselist")
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query = query.filter(attr.contains(v))
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else:
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logger.debug("Single item.")
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query = query.filter(attr == v)
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if k in singles:
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logger.warning(f"{k} is in singles. Returning only one value.")
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limit = 1
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if offset:
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query.offset(offset)
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with query.session.no_autoflush:
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match limit:
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case 0:
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@@ -476,13 +487,13 @@ class BaseClass(Base):
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# logger.debug(f"Attempting to set: {key} to {value}")
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if key.startswith("_"):
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return super().__setattr__(key, value)
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try:
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check = not hasattr(self, key)
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except:
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return
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# try:
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check = not hasattr(self, key)
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# except:
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# return
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if check:
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try:
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json.dumps(value)
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value = json.dumps(value)
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except TypeError:
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value = str(value)
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self._misc_info.update({key: value})
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@@ -612,6 +623,7 @@ class BaseClass(Base):
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if dlg.exec():
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pass
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class LogMixin(Base):
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tracking_exclusion: ClassVar = ['artic_technician', 'clientsubmissionsampleassociation',
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'submission_reagent_associations', 'submission_equipment_associations',
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@@ -149,12 +149,14 @@ class ClientSubmission(BaseClass, LogMixin):
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pass
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# query = query.order_by(cls.submitted_date.desc())
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# NOTE: Split query results into pages of size {page_size}
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if page_size > 0:
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query = query.limit(page_size)
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if page_size > 0 and limit == 0:
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limit = page_size
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page = page - 1
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if page is not None:
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query = query.offset(page * page_size)
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return cls.execute_query(query=query, limit=limit, **kwargs)
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offset = page * page_size
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else:
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offset = None
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return cls.execute_query(query=query, limit=limit, offset=offset, **kwargs)
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@classmethod
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def submissions_to_df(cls, submissiontype: str | None = None, limit: int = 0,
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@@ -269,7 +271,9 @@ class ClientSubmission(BaseClass, LogMixin):
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try:
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assert isinstance(sample, Sample)
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except AssertionError:
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logger.warning(f"Converting {sample} to sql.")
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sample = sample.to_sql()
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logger.debug(sample.__dict__)
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try:
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row = sample._misc_info['row']
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except (KeyError, AttributeError):
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@@ -278,10 +282,12 @@ class ClientSubmission(BaseClass, LogMixin):
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column = sample._misc_info['column']
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except KeyError:
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column = 0
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logger.debug(f"Sample: {sample}")
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submission_rank = sample._misc_info['submission_rank']
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assoc = ClientSubmissionSampleAssociation(
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sample=sample,
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submission=self,
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submission_rank=sample._misc_info['submission_rank'],
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submission_rank=submission_rank,
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row=row,
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column=column
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)
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@@ -310,8 +316,9 @@ class ClientSubmission(BaseClass, LogMixin):
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for sample in active_samples:
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sample = sample.to_sql()
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logger.debug(f"Sample: {sample.id}")
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assoc = run.add_sample(sample)
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assoc.save()
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if sample not in run.sample:
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assoc = run.add_sample(sample)
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assoc.save()
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else:
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logger.warning("Run cancelled.")
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obj.set_data()
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