Writer beginnings

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

@@ -18,7 +18,10 @@ from sqlalchemy.exc import ArgumentError
 from typing import Any, List, ClassVar
 from pathlib import Path
 from sqlalchemy.orm.relationships import _RelationshipDeclared
+
+from frontend import select_save_file
 from tools import report_result, list_sort_dict
+from backend.excel import writers
 
 # NOTE: Load testing environment
 if 'pytest' in sys.modules:
@@ -241,6 +244,7 @@ class BaseClass(Base):
         allowed = [k for k, v in cls.__dict__.items() if isinstance(v, InstrumentedAttribute) or isinstance(v, hybrid_property)]
         # and not isinstance(v.property, _RelationshipDeclared)]
         sanitized_kwargs = {k: v for k, v in kwargs.items() if k in allowed}
+        outside_kwargs = {k: v for k, v in kwargs.items() if k not in allowed}
         logger.debug(f"Sanitized kwargs: {sanitized_kwargs}")
         instance = cls.query(**sanitized_kwargs)
         if not instance or isinstance(instance, list):
@@ -258,6 +262,7 @@ class BaseClass(Base):
                     setattr(instance, k, v.to_sql())
                 else:
                     logger.error(f"Could not set {k} due to {e}")
+        instance._misc_info.update(outside_kwargs)
         logger.info(f"Instance from query or create: {instance}, new: {new}")
         return instance, new
 
@@ -309,10 +314,16 @@ class BaseClass(Base):
                 check = False
             if check:
                 logger.debug("Got uselist")
-                query = query.filter(attr.contains(v))
+                try:
+                    query = query.filter(attr.contains(v))
+                except ArgumentError:
+                    continue
             else:
                 logger.debug("Single item.")
-                query = query.filter(attr == v)
+                try:
+                    query = query.filter(attr == v)
+                except ArgumentError:
+                    continue
             if k in singles:
                 logger.warning(f"{k} is in singles. Returning only one value.")
                 limit = 1
@@ -496,7 +507,10 @@ class BaseClass(Base):
                 value = json.dumps(value)
             except TypeError:
                 value = str(value)
-            self._misc_info.update({key: value})
+            try:
+                self._misc_info.update({key: value})
+            except AttributeError:
+                self._misc_info = {key: value}
             return
         try:
             field_type = getattr(self.__class__, key)
@@ -623,6 +637,17 @@ class BaseClass(Base):
         if dlg.exec():
             pass
 
+    def export(self, obj, output_filepath: str|Path|None=None):
+        if not hasattr(self, "template_file"):
+            logger.error(f"Export not implemented for {self.__class__.__name__}")
+            return
+        pyd = self.to_pydantic()
+        if not output_filepath:
+            output_filepath = select_save_file(obj=obj, default_name=pyd.construct_filename(), extension="xlsx")
+        Writer = getattr(writers, f"{self.__class__.__name__}Writer")
+        writer = Writer(output_filepath=output_filepath, pydant_obj=pyd, range_dict=self.range_dict)
+        workbook = writer
+
 
 class LogMixin(Base):
     tracking_exclusion: ClassVar = ['artic_technician', 'clientsubmissionsampleassociation',

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

@@ -15,6 +15,8 @@ from operator import itemgetter
 from pprint import pformat
 from pandas import DataFrame
 from sqlalchemy.ext.hybrid import hybrid_property
+
+from frontend import select_save_file
 from . import Base, BaseClass, Reagent, SubmissionType, KitType, ClientLab, Contact, LogMixin, Procedure, kittype_procedure
 from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, func, Table, Sequence
 from sqlalchemy.orm import relationship, validates, Query
@@ -158,6 +160,14 @@ class ClientSubmission(BaseClass, LogMixin):
             offset = None
         return cls.execute_query(query=query, limit=limit, offset=offset, **kwargs)
 
+    @property
+    def template_file(self):
+        return self.submissiontype.template_file
+
+    @property
+    def range_dict(self):
+        return self.submissiontype.info_map
+
     @classmethod
     def submissions_to_df(cls, submissiontype: str | None = None, limit: int = 0,
                           chronologic: bool = True, page: int = 1, page_size: int = 250) -> pd.DataFrame:
@@ -318,12 +328,12 @@ class ClientSubmission(BaseClass, LogMixin):
                 logger.debug(f"Sample: {sample.id}")
                 if sample not in run.sample:
                     assoc = run.add_sample(sample)
-                    assoc.save()
+                    # assoc.save()
+            run.save()
         else:
             logger.warning("Run cancelled.")
         obj.set_data()
 
-
     def edit(self, obj):
         logger.debug("Edit")
 
@@ -352,6 +362,9 @@ class ClientSubmission(BaseClass, LogMixin):
         output['expanded'] = ["clientlab", "contact", "submissiontype"]
         return output
 
+    def to_pydantic(self, filepath: Path|str|None=None, **kwargs):
+        output = super().to_pydantic(filepath=filepath, **kwargs)
+        return output
 
 class Run(BaseClass, LogMixin):
     """
@@ -1266,6 +1279,15 @@ class Run(BaseClass, LogMixin):
             self.set_attribute(key='comment', value=comment)
             self.save(original=False)
 
+    def export(self, obj, output_filepath: str|Path|None=None):
+
+        clientsubmission_pyd = self.clientsubmission.to_pydantic()
+        if not output_filepath:
+            output_filepath = select_save_file(obj=obj, default_name=clientsubmission_pyd.construct_filename(), extension="xlsx")
+        Writer = getattr(writers, "ClientSubmissionWriter")
+        writer = Writer(output_filepath=output_filepath, pydant_obj=pyd, range_dict=self.range_dict)
+        workbook = writer.
+
     def backup(self, obj=None, fname: Path | None = None, full_backup: bool = False):
         """
         Exports xlsx info files for this instance.
@@ -1890,8 +1912,8 @@ class RunSampleAssociation(BaseClass):
     # id = Column(INTEGER, unique=True, nullable=False)  #: id to be used for inheriting purposes
     sample_id = Column(INTEGER, ForeignKey("_sample.id"), primary_key=True)  #: id of associated sample
     run_id = Column(INTEGER, ForeignKey("_run.id"), primary_key=True)  #: id of associated procedure
-    row = Column(INTEGER)  #: row on the 96 well plate
-    column = Column(INTEGER)  #: column on the 96 well plate
+    # row = Column(INTEGER)  #: row on the 96 well plate
+    # column = Column(INTEGER)  #: column on the 96 well plate
     # misc_info = Column(JSON)
 
     # NOTE: reference to the Submission object