Qubit sample results now written to export.

CHANGELOG.md

@@ -1,3 +1,7 @@
+# 202510.01
+
+- Update for Python 3.13
+
 # 202509.04
 
 - Qubit results parsing complete.

src/submissions/backend/db/models/__init__.py

@@ -48,10 +48,10 @@ class BaseClass(Base):
         except AttributeError:
             return f"<{self.__class__.__name__}(Name Unavailable)>"
 
-    # @classproperty
+
-    @classmethod
     @declared_attr
-    def aliases(cls) -> List[str]:
+    @classmethod
+    def aliases(cls):
         """
         List of other names this class might be known by.
 
@@ -60,9 +60,9 @@ class BaseClass(Base):
         """
         return [cls.query_alias]
 
-    @classmethod
     @declared_attr
-    def query_alias(cls) -> str:
+    @classmethod
+    def query_alias(cls):
         """
         What to query this class as.
 
@@ -71,8 +71,8 @@ class BaseClass(Base):
         """
         return cls.__name__.lower()
 
-    @classmethod
     @declared_attr
+    @classmethod
     def __tablename__(cls) -> str:
         """
         Sets table name to lower case class name.
@@ -82,8 +82,8 @@ class BaseClass(Base):
         """
         return f"_{cls.__name__.lower()}"
 
-    @classmethod
     @declared_attr
+    @classmethod
     def __database_session__(cls) -> Session:
         """
         Pull db session from ctx to be used in operations
@@ -93,8 +93,8 @@ class BaseClass(Base):
         """
         return ctx.database_session
 
-    @classmethod
     @declared_attr
+    @classmethod
     def __directory_path__(cls) -> Path:
         """
         Pull directory path from ctx to be used in operations.
@@ -104,8 +104,8 @@ class BaseClass(Base):
         """
         return ctx.directory_path
 
-    @classmethod
     @declared_attr
+    @classmethod
     def __backup_path__(cls) -> Path:
         """
         Pull backup directory path from ctx to be used in operations.
@@ -119,10 +119,9 @@ class BaseClass(Base):
         super().__init__(*args, **kwargs)
         self._misc_info = dict()
 
-    # @classproperty
-    @classmethod
     @declared_attr
-    def jsons(cls) -> List[str]:
+    @classmethod
+    def jsons(cls):
         """
         Get list of JSON db columns
 
@@ -134,10 +133,9 @@ class BaseClass(Base):
         except AttributeError:
             return []
 
-    # @classproperty
-    @classmethod
     @declared_attr
-    def timestamps(cls) -> List[str]:
+    @classmethod
+    def timestamps(cls):
         """
         Get list of TIMESTAMP columns
 
@@ -392,10 +390,9 @@ class BaseClass(Base):
             pass
         return dicto
 
-    # @classproperty
-    @classmethod
     @declared_attr
-    def pydantic_model(cls) -> BaseModel:
+    @classmethod
+    def pydantic_model(cls):
         """
         Gets the pydantic model corresponding to this object.
 
@@ -414,9 +411,9 @@ class BaseClass(Base):
         return model
 
     # @classproperty
-    @classmethod
     @declared_attr
-    def add_edit_tooltips(cls) -> dict:
+    @classmethod
+    def add_edit_tooltips(cls):
         """
         Gets tooltips for Omni-add-edit
 
@@ -425,10 +422,9 @@ class BaseClass(Base):
         """
         return dict()
 
-    # @classproperty
-    @classmethod
     @declared_attr
-    def details_template(cls) -> Template:
+    @classmethod
+    def details_template(cls):
         """
         Get the details jinja template for the correct class
 
@@ -660,6 +656,7 @@ class BaseClass(Base):
             pyd = getattr(pydant, pyd_model_name)
         except AttributeError:
             raise AttributeError(f"Could not get pydantic class {pyd_model_name}")
+        pyd.model_rebuild()
         return pyd(**self.details_dict(**kwargs))
 
     def show_details(self, obj):
@@ -699,6 +696,7 @@ class ConfigItem(BaseClass):
     """
     Key:JSON objects to store config settings in database. 
     """
+
     id = Column(INTEGER, primary_key=True)
     key = Column(String(32))  #: Name of the configuration item.
     value = Column(JSON)  #: Value associated with the config item.

src/submissions/backend/db/models/submissions.py

@@ -1937,6 +1937,8 @@ class ProcedureSampleAssociation(BaseClass):
 
     def to_pydantic(self, **kwargs):
         output = super().to_pydantic(pyd_model_name="PydSample")
+        # from backend.validators.pydant import PydSample
+        # output = PydSample(**self.details_dict(**kwargs))
         try:
             output.submission_rank = output.misc_info['submission_rank']
         except KeyError:

src/submissions/backend/validators/__init__.py

@@ -1,15 +1,18 @@
 """
 Contains all validators
 """
+from __future__ import annotations
 import logging, re
 import sys
 from pathlib import Path
 from openpyxl import load_workbook
-from backend.db.models import Run, SubmissionType
 from tools import jinja_template_loading
 from jinja2 import Template
 from dateutil.parser import parse
 from datetime import datetime
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    from backend.db.models import SubmissionType
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -27,15 +30,17 @@ class DefaultNamer(object):
 
 class ClientSubmissionNamer(DefaultNamer):
 
-    def __init__(self, filepath: str | Path, submissiontype: str|SubmissionType|None=None,
+    def __init__(self, filepath: str | Path, submissiontype: str|"SubmissionType"|None=None,
                  data: dict | None = None, **kwargs):
+        from backend.db.models import SubmissionType
         super().__init__(filepath=filepath)
         if not submissiontype:
-            submissiontype = self.retrieve_submissiontype(filepath=self.filepath)
+            self.submissiontype = self.retrieve_submissiontype(filepath=self.filepath)
         if isinstance(submissiontype, str):
-            submissiontype = SubmissionType.query(name=submissiontype)
+            self.submissiontype = SubmissionType.query(name=submissiontype)
 
-    def retrieve_submissiontype(self, filepath: str | Path):
+    def retrieve_submissiontype(self):
+        from backend.db.models import SubmissionType
         # NOTE: Attempt 1, get from form properties:
         sub_type = self.get_subtype_from_properties()
         if not sub_type:
@@ -51,6 +56,7 @@ class ClientSubmissionNamer(DefaultNamer):
         return sub_type
 
     def get_subtype_from_regex(self) -> SubmissionType:
+        from backend.db.models import SubmissionType
         regex = SubmissionType.regex
         m = regex.search(self.filepath.__str__())
         try:
@@ -64,6 +70,7 @@ class ClientSubmissionNamer(DefaultNamer):
 
     def get_subtype_from_preparse(self) -> SubmissionType:
         from backend.excel.parsers.clientsubmission_parser import ClientSubmissionInfoParser
+        from backend.db.models import SubmissionType
         parser = ClientSubmissionInfoParser(self.filepath)
         sub_type = next((value for k, value in parser.parsed_info.items() if k == "submissiontype"), None)
         sub_type = SubmissionType.query(name=sub_type)
@@ -72,6 +79,7 @@ class ClientSubmissionNamer(DefaultNamer):
         return sub_type
 
     def get_subtype_from_properties(self) -> SubmissionType:
+        from backend.db.models import SubmissionType
         wb = load_workbook(self.filepath)
         # NOTE: Gets first category in the metadata.
         categories = wb.properties.category.split(";")
@@ -88,6 +96,7 @@ class RSLNamer(object):
     """
 
     def __init__(self, filename: str, submission_type: str | None = None, data: dict | None = None):
+        from backend.db.models import SubmissionType
         # NOTE: Preferred method is path retrieval, but might also need validation for just string.
         filename = Path(filename) if Path(filename).exists() else filename
         self.submission_type = submission_type
@@ -113,7 +122,7 @@ class RSLNamer(object):
         Returns:
             str: parsed procedure type
         """
-
+        from backend.db.models import SubmissionType
         def st_from_path(filepath: Path) -> str:
             """
             Sub def to get proceduretype from a file path
@@ -186,8 +195,9 @@ class RSLNamer(object):
             regex (str): string to construct pattern
             filename (str): string to be parsed
         """
+        from backend.db.models import Run
         if regex is None:
-            regex = BasicRun.regex
+            regex = Run.regex
         match filename:
             case Path():
                 m = regex.search(filename.stem)
@@ -215,6 +225,7 @@ class RSLNamer(object):
         Returns:
             str: Output filename
         """
+        from backend.db.models import Run
         if "submitted_date" in data.keys():
             if isinstance(data['submitted_date'], dict):
                 if data['submitted_date']['value'] is not None:

src/submissions/backend/validators/pydant.py

@@ -135,6 +135,47 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
                     continue
         return list(set(output))
 
+class PydResults(PydBaseClass, arbitrary_types_allowed=True):
+    result: dict = Field(default={})
+    result_type: str = Field(default="NA")
+    img: None | bytes = Field(default=None)
+    # parent: Procedure | ProcedureSampleAssociation | None = Field(default=None)
+    parent: Any | None = Field(default=None)
+    date_analyzed: datetime | None = Field(default=None)
+
+    @field_validator("date_analyzed")
+    @classmethod
+    def set_today(cls, value):
+        match value:
+            case str():
+                value = datetime.strptime(value, "%Y-%m-%d %H:%M:%S")
+            case datetime():
+                pass
+            case date():
+                value = datetime.combine(value, datetime.max.time())
+            case _:
+                value = datetime.now()
+        return value
+
+    def to_sql(self):
+        sql, _ = Results.query_or_create(result_type=self.result_type, result=self.results)
+        try:
+            check = sql.image
+        except FileNotFoundError:
+            check = False
+        if not check:
+            sql.image = self.img
+        if not sql.date_analyzed:
+            sql.date_analyzed = self.date_analyzed
+        match self.parent:
+            case ProcedureSampleAssociation():
+                sql.sampleprocedureassociation = self.parent
+            case Procedure():
+                sql.procedure = self.parent
+            case _:
+                logger.error("Improper association found.")
+        return sql
+
 
 class PydReagentLot(PydBaseClass):
     lot: str | None
@@ -1623,42 +1664,42 @@ class PydRun(PydBaseClass):  #, extra='allow'):
         return samples
 
 
-class PydResults(PydBaseClass, arbitrary_types_allowed=True):
+# class PydResults(PydBaseClass, arbitrary_types_allowed=True):
-    result: dict = Field(default={})
+#     result: dict = Field(default={})
-    result_type: str = Field(default="NA")
+#     result_type: str = Field(default="NA")
-    img: None | bytes = Field(default=None)
+#     img: None | bytes = Field(default=None)
-    parent: Procedure | ProcedureSampleAssociation | None = Field(default=None)
+#     parent: Procedure | ProcedureSampleAssociation | None = Field(default=None)
-    date_analyzed: datetime | None = Field(default=None)
+#     date_analyzed: datetime | None = Field(default=None)
-
+#
-    @field_validator("date_analyzed")
+#     @field_validator("date_analyzed")
-    @classmethod
+#     @classmethod
-    def set_today(cls, value):
+#     def set_today(cls, value):
-        match value:
+#         match value:
-            case str():
+#             case str():
-                value = datetime.strptime(value, "%Y-%m-%d %H:%M:%S")
+#                 value = datetime.strptime(value, "%Y-%m-%d %H:%M:%S")
-            case datetime():
+#             case datetime():
-                pass
+#                 pass
-            case date():
+#             case date():
-                value = datetime.combine(value, datetime.max.time())
+#                 value = datetime.combine(value, datetime.max.time())
-            case _:
+#             case _:
-                value = datetime.now()
+#                 value = datetime.now()
-        return value
+#         return value
-
+#
-    def to_sql(self):
+#     def to_sql(self):
-        sql, _ = Results.query_or_create(result_type=self.result_type, result=self.results)
+#         sql, _ = Results.query_or_create(result_type=self.result_type, result=self.results)
-        try:
+#         try:
-            check = sql.image
+#             check = sql.image
-        except FileNotFoundError:
+#         except FileNotFoundError:
-            check = False
+#             check = False
-        if not check:
+#         if not check:
-            sql.image = self.img
+#             sql.image = self.img
-        if not sql.date_analyzed:
+#         if not sql.date_analyzed:
-            sql.date_analyzed = self.date_analyzed
+#             sql.date_analyzed = self.date_analyzed
-        match self.parent:
+#         match self.parent:
-            case ProcedureSampleAssociation():
+#             case ProcedureSampleAssociation():
-                sql.sampleprocedureassociation = self.parent
+#                 sql.sampleprocedureassociation = self.parent
-            case Procedure():
+#             case Procedure():
-                sql.procedure = self.parent
+#                 sql.procedure = self.parent
-            case _:
+#             case _:
-                logger.error("Improper association found.")
+#                 logger.error("Improper association found.")
-        return sql
+#         return sql

src/submissions/tools/__init__.py

@@ -782,7 +782,8 @@ def yaml_regex_creator(loader, node):
     nodes = loader.construct_sequence(node)
     name = nodes[0].replace(" ", "_")
     abbr = nodes[1]
-    return f"(?P<{name}>RSL(?:-|_)?{abbr}(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
+    # return f"(?P<{name}>RSL(?:-|_)?{abbr}(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
+    return f"(?P<{name}>RSL(?:-|_)?{abbr}(?:-|_)?20\\d{2}-?\\d{2}-?\\d{2}(?:(_|-)?\\d?([^_0123456789\\sA-QS-Z]|$)?R?\\d?)?)"
 
 
 def super_splitter(ins_str: str, substring: str, idx: int) -> str: