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
+    # row = Column(INTEGER)  #: row on the 96 well plate
-    column = Column(INTEGER)  #: column on the 96 well plate
+    # column = Column(INTEGER)  #: column on the 96 well plate
     # misc_info = Column(JSON)
 
     # NOTE: reference to the Submission object

src/submissions/backend/excel/parsers/__init__.py

@@ -5,6 +5,8 @@ from __future__ import annotations
 import logging, re
 from pathlib import Path
 from typing import Generator, Tuple, TYPE_CHECKING
+
+from openpyxl.reader.excel import load_workbook
 from pandas import DataFrame
 from backend.validators import pydant
 if TYPE_CHECKING:
@@ -78,8 +80,6 @@ class DefaultKEYVALUEParser(DefaultParser):
         sheet="Sample List"
     )]
 
-
-
     @property
     def parsed_info(self) -> Generator[Tuple, None, None]:
         for item in self.range_dict:
@@ -91,7 +91,10 @@ class DefaultKEYVALUEParser(DefaultParser):
                     key = re.sub(r"\(.*\)", "", key)
                     key = key.lower().replace(":", "").strip().replace(" ", "_")
                     value = item['worksheet'].cell(row, item['value_column']).value
-                    value = dict(value=value, missing=False if value else True)
+                    missing = False if value else True
+                    location_map = dict(row=row, key_column=item['key_column'], value_column=item['value_column'], sheet=item['sheet'])
+                    value = dict(value=value, location=location_map, missing=missing)
+                    logger.debug(f"Yieldings {value} for {key}")
                     yield key, value
 
 
@@ -126,5 +129,5 @@ class DefaultTABLEParser(DefaultParser):
     def to_pydantic(self, **kwargs):
         return [self._pyd_object(**output) for output in self.parsed_info]
 
-from .clientsubmission_parser import *
+from .clientsubmission_parser import ClientSubmissionSampleParser, ClientSubmissionInfoParser
 from backend.excel.parsers.results_parsers.pcr_results_parser import PCRInfoParser, PCRSampleParser

src/submissions/backend/excel/parsers/clientsubmission_parser.py

@@ -96,8 +96,6 @@ class ClientSubmissionInfoParser(DefaultKEYVALUEParser, SubmissionTyperMixin):
                 # TODO: check if run with name already exists
                 add_run = QuestionAsker(title="Add Run?", message="We've detected a sheet corresponding to an associated procedure type.\nWould you like to add a new run?")
                 if add_run.accepted:
-
-
                 # NOTE: recruit parser.
                     try:
                         manager = getattr(procedure_managers, name)

src/submissions/backend/validators/pydant.py

@@ -27,6 +27,7 @@ logger = logging.getLogger(f"procedure.{__name__}")
 
 class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
     _sql_object: ClassVar = None
+    # _misc_info: dict|None = None
 
     @model_validator(mode="before")
     @classmethod
@@ -67,6 +68,10 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
     def __init__(self, **data):
         # NOTE: Grab the sql model for validation purposes.
         self.__class__._sql_object = getattr(models, self.__class__.__name__.replace("Pyd", ""))
+        # try:
+        #     self.template_file = self.__class__._sql_object.template_file
+        # except AttributeError:
+        #     pass
         super().__init__(**data)
 
     def filter_field(self, key: str) -> Any:
@@ -105,6 +110,12 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
             output = {k: getattr(self, k) for k in fields}
         else:
             output = {k: self.filter_field(k) for k in fields}
+        if hasattr(self, "misc_info") and "info_placement" in self.misc_info:
+            for k, v in output.items():
+                try:
+                    output[k]['location'] = [item['location'] for item in self.misc_info['info_placement'] if item['name'] == k]
+                except (TypeError, KeyError):
+                    continue
         return output
 
     def to_sql(self):
@@ -301,6 +312,7 @@ class PydSample(PydBaseClass):
         sql._misc_info["submission_rank"] = self.submission_rank
         return sql
 
+
 class PydTips(BaseModel):
     name: str
     lot: str | None = Field(default=None)
@@ -1662,7 +1674,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
 class PydClientSubmission(PydBaseClass):
     # sql_object: ClassVar = ClientSubmission
 
-    filepath: Path
+    filepath: Path | None = Field(default=None)
     submissiontype: dict | None
     submitted_date: dict | None = Field(default=dict(value=date.today(), missing=True), validate_default=True)
     clientlab: dict | None
@@ -1673,6 +1685,39 @@ class PydClientSubmission(PydBaseClass):
     contact: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
     submitter_plate_id: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
 
+    @field_validator("submitted_date", mode="before")
+    @classmethod
+    def enforce_submitted_date(cls, value):
+        match value:
+            case str():
+                value = dict(value=datetime.strptime(value, "%Y-%m-%d %H:%M:%S"), missing=False)
+            case date() | datetime():
+                value = dict(value=value, missing=False)
+            case _:
+                pass
+        return value
+
+    @field_validator("submitter_plate_id", mode="before")
+    @classmethod
+    def enforce_submitter_plate_id(cls, value):
+        if isinstance(value, str):
+            value = dict(value=value, missing=False)
+        return value
+
+    @field_validator("submission_category", mode="before")
+    @classmethod
+    def enforce_submission_category_id(cls, value):
+        if isinstance(value, str):
+            value = dict(value=value, missing=False)
+        return value
+
+    @field_validator("sample_count", mode="before")
+    @classmethod
+    def enforce_sample_count(cls, value):
+        if isinstance(value, str) or isinstance(value, int):
+            value = dict(value=value, missing=False)
+        return value
+
     @field_validator("sample_count")
     @classmethod
     def enforce_integer(cls, value):
@@ -1700,7 +1745,7 @@ class PydClientSubmission(PydBaseClass):
         except TypeError:
             check = True
         if check:
-            return dict(value=date.today(), missing=True)
+            value.update(dict(value=date.today(), missing=True))
         else:
             match value['value']:
                 case str():
@@ -1735,6 +1780,29 @@ class PydClientSubmission(PydBaseClass):
         from frontend.widgets.submission_widget import ClientSubmissionFormWidget
         return ClientSubmissionFormWidget(parent=parent, clientsubmission=self, samples=samples, disable=disable)
 
+    def to_sql(self):
+        sql = super().to_sql()
+        if "info_placement" not in sql._misc_info:
+            sql._misc_info['info_placement'] = []
+        info_placement = []
+        for k in list(self.model_fields.keys()) + list(self.model_extra.keys()):
+            attribute = getattr(self, k)
+            match k:
+                case "filepath":
+                    sql._misc_info[k] = attribute.__str__()
+                    continue
+                case _:
+                    pass
+            logger.debug(f"Setting {k} to {attribute}")
+            if isinstance(attribute, dict):
+                if "location" in attribute:
+                    info_placement.append(dict(name=k, location=attribute['location']))
+                else:
+                    info_placement.append(dict(name=k, location=None))
+        max_row = max([value['location']['row'] for value in info_placement if value])
+        sql._misc_info['info_placement'] = info_placement
+        return sql
+
 
 class PydResults(PydBaseClass, arbitrary_types_allowed=True):
     results: dict = Field(default={})

src/submissions/frontend/widgets/sample_checker.py

@@ -35,8 +35,8 @@ class SampleChecker(QDialog):
         self.channel = QWebChannel()
         self.channel.registerObject('backend', self)
         # NOTE: Used to maintain javascript functions.
-        template = env.get_template("sample_checker.html")
+        # template = env.get_template("sample_checker.html")
-        template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
+        # template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
         # with open(template_path.joinpath("css", "styles.css"), "r") as f:
         #     css = [f.read()]
         try:

src/submissions/frontend/widgets/submission_widget.py

@@ -472,6 +472,10 @@ class SubmissionFormWidget(QWidget):
                 self.missing: bool = value['missing']
             except (TypeError, KeyError):
                 self.missing: bool = True
+            try:
+                self.location: dict|None = value['location']
+            except (TypeError, KeyError):
+                self.location: dict|None = None
             if self.input is not None:
                 layout.addWidget(self.label)
                 layout.addWidget(self.input)
@@ -501,7 +505,7 @@ class SubmissionFormWidget(QWidget):
                     value = self.input.date().toPyDate()
                 case _:
                     return None, None
-            return self.input.objectName(), dict(value=value, missing=self.missing)
+            return self.input.objectName(), dict(value=value, missing=self.missing, location=self.location)
 
         def set_widget(self, parent: QWidget, key: str, value: dict,
                        submission_type: str | SubmissionType | None = None,
@@ -518,6 +522,7 @@ class SubmissionFormWidget(QWidget):
             Returns:
                 QWidget: Form object
             """
+
             if isinstance(submission_type, str):
                 submission_type = SubmissionType.query(name=submission_type)
             if sub_obj is None:
@@ -843,6 +848,7 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
                 value = getattr(self, item)
                 info[item] = value
         for k, v in info.items():
+            logger.debug(f"Setting pyd {k} to {v}")
             self.pyd.__setattr__(k, v)
         report.add_result(report)
         return report

src/submissions/templates/bacterialculture_details.html

@@ -1,28 +0,0 @@
-{% extends "basicsubmission_details.html" %}
-
-<head>
-    {% block head %}
-    {{ super() }}
-    {% endblock %}
-</head>
-
-<body>
-    {% block body %}
-    {{ super() }}
-    {% if sub['controls'] %}
-        <h3><u>Attached Controls:</u></h3>
-        {% for item in sub['controls'] %}
-            <p>&nbsp;&nbsp;&nbsp;<b>{{ item['name'] }}:</b> {{ item['type'] }} (Targets: {{ item['targets'] }})</p>
-            {% if item['kraken'] %}
-                <p>&nbsp;&nbsp;&nbsp;{{ item['name'] }} Top 10 Kraken Results:</p>
-                <p>{% for genera in item['kraken'] %}
-                    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;{{ genera['name'] }}: {{ genera['kraken_count'] }} ({{ genera['kraken_percent'] }})<br>
-                {% endfor %}</p>
-            {% endif %}
-        {% endfor %}
-    {% endif %}
-    {% endblock %}
-    {% block signing_button %}
-    {{ super() }}
-    {% endblock %}
-</body>

src/submissions/templates/equipment_details.html

@@ -10,12 +10,8 @@
     <h2><u>Equipment Details for {{ equipment['name'] }}</u></h2>
     {{ super() }}
     <p>{% for key, value in equipment.items() if key not in equipment['excluded'] %}
-<!--        &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title }}: </b>{% if permission and key in reagent['editable']%}<input type={% if key=='expiry' %}"date"{% else %}"text"{% endif %} id="{{ key }}" name="{{ key }}" value="{{ value }}">{% else %}{{ value }}{% endif %}<br>-->
         &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title }}: </b>{{ value }}<br>
     {% endfor %}</p>
-<!--    {% if permission %}-->
-<!--        <button type="button" id="save_btn">Save</button>-->
-<!--    {% endif %}-->
     {% if equipment['submissions'] %}<h2>Submissions:</h2>
         {% for submission in equipment['submissions'] %}
         <p><b><a class="data-link" id="{{ submission['plate'] }}">{{ submission['plate'] }}:</a></b> <a class="data-link process" id="{{ submission['process'] }}">{{ submission['process'] }}</a></p>

src/submissions/templates/support/tooltip.html

@@ -1,4 +1,4 @@
 Sample name: {{ fields['submitter_id'] }}<br>
 {% if fields['organism'] %}Organism: {{ fields['organism'] }}<br>{% endif %}
 {% if fields['concentration'] %}Concentration: {{ fields['concentration'] }}<br>{% endif %}
-Well: {{ fields['well'] }}<!--{{ fields['column'] }}-->
+Well: {{ fields['well'] }}

src/submissions/templates/wastewater_details.html

@@ -1,37 +0,0 @@
-{% extends "basicsubmission_details.html" %}
-
-<head>
-    {% block head %}
-    {{ super() }}
-    {% endblock %}
-</head>
-
-<body>
-    {% block body %}
-    {{ super() }}
-    {% if sub['pcr_info'] %}
-        {% for entry in sub['pcr_info'] %}
-        {% if 'comment' not in entry.keys() %}
-            <h3><u>qPCR Momentum Status:</u></h3>
-        {% else %}
-            <h3><u>qPCR Status:</u></h3>
-        {% endif %}
-        <p>{% for key, value in entry.items() if key != 'imported_by'%}
-            {% if "column" in key %}
-                &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key|replace('_', ' ')|title() }}:</b> {{ value }}uL<br>
-            {% else %}
-                &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key|replace('_', ' ')|title() }}:</b> {{ value }}<br>
-            {% endif %}
-        {% endfor %}</p>
-        {% endfor %}
-        {% endif %}
-     {% if sub['origin_plate'] %}
-    <br/>
-    <h3><u>24 Well Plate:</u></h3>
-    {{ sub['origin_plate'] }}
-    {% endif %}
-    {% endblock %}
-    {% block signing_button %}
-    {{ super() }}
-    {% endblock %}
-</body>

src/submissions/templates/wastewaterartic_details.html

@@ -1,41 +0,0 @@
-{% extends "basicsubmission_details.html" %}
-
-<head>
-    {% block head %}
-    {{ super() }}
-    {% endblock %}
-</head>
-
-<body>
-    {% block body %}
-    {{ super() }}
-    {% if sub['gel_info'] %}
-    <br/>
-    <h3><u>Gel Box:</u></h3>
-    {% if sub['gel_image_actual'] %}
-        <br/>
-        <img align='left' height="400px" width="600px" src="data:image/jpeg;base64,{{ sub['gel_image_actual'] | safe }}">
-    {% endif %}
-    <br/>
-        <table style="width:100%; border: 1px solid black; border-collapse: collapse;">
-            <tr>
-            {% for header in sub['headers'] %}
-                <th>{{ header }}</th>
-            {% endfor %}
-            </tr>
-            {% for field in sub['gel_info'] %}
-            <tr>
-                <td>{{ field['name'] }}</td>
-                {% for item in field['values'] %}
-                <td>{{ item['value'] }}</td>
-                {% endfor %}
-            </tr>
-            {% endfor %}
-        </table>    
-    <br/>    
-    {% endif %}
-    {% endblock %}
-    {% block signing_button %}
-    {{ super() }}
-    {% endblock %}
-</body>