Mid documentation and code clean-up.

CHANGELOG.md

@@ -1,5 +1,6 @@
 ## 202406.04
 
+- Exported submission details will now be in docx format.
 - Adding in tips to Equipment usage.
 - New WastewaterArticAssociation will track previously missed sample info.
 

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

@@ -112,7 +112,7 @@ class BaseClass(Base):
     @classmethod
     def execute_query(cls, query: Query = None, model=None, limit: int = 0, **kwargs) -> Any | List[Any]:
         """
-        Execute sqlalchemy query.
+        Execute sqlalchemy query with relevant defaults.
 
         Args:
             model (Any, optional): model to be queried. Defaults to None
@@ -137,6 +137,7 @@ class BaseClass(Base):
             except (ArgumentError, AttributeError) as e:
                 logger.error(f"Attribute {k} unavailable due to:\n\t{e}\nSkipping.")
             if k in singles:
+                logger.warning(f"{k} is in singles. Returning only one value.")
                 limit = 1
         with query.session.no_autoflush:
             match limit:
@@ -165,8 +166,8 @@ class ConfigItem(BaseClass):
     Key:JSON objects to store config settings in database. 
     """    
     id = Column(INTEGER, primary_key=True)
-    key = Column(String(32))
+    key = Column(String(32)) #: Name of the configuration item.
-    value = Column(JSON)
+    value = Column(JSON) #: Value associated with the config item.
 
     def __repr__(self):
         return f"ConfigItem({self.key} : {self.value})"

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

@@ -55,7 +55,7 @@ class ControlType(BaseClass):
 
     def get_subtypes(self, mode: str) -> List[str]:
         """
-        Get subtypes associated with this controltype
+        Get subtypes associated with this controltype (currently used only for Kraken)
 
         Args:
             mode (str): analysis mode name
@@ -140,15 +140,11 @@ class Control(BaseClass):
             kraken = {}
         # logger.debug("calculating kraken count total to use in percentage")
         kraken_cnt_total = sum([kraken[item]['kraken_count'] for item in kraken])
-        new_kraken = []
+        # logger.debug("Creating new kraken.")
-        for item in kraken:
+        new_kraken = [dict(name=item, kraken_count=kraken[item]['kraken_count'], kraken_percent="{0:.0%}".format(kraken[item]['kraken_count'] / kraken_cnt_total)) for item in kraken]
-            # logger.debug("calculating kraken percent (overwrites what's already been scraped)")
-            kraken_percent = kraken[item]['kraken_count'] / kraken_cnt_total
-            new_kraken.append({'name': item, 'kraken_count': kraken[item]['kraken_count'],
-                               'kraken_percent': "{0:.0%}".format(kraken_percent)})
         new_kraken = sorted(new_kraken, key=itemgetter('kraken_count'), reverse=True)
         # logger.debug("setting targets")
-        if self.controltype.targets == []:
+        if not self.controltype.targets:
             targets = ["None"]
         else:
             targets = self.controltype.targets

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

@@ -70,6 +70,7 @@ kittypes_processes = Table(
     extend_existing=True
 )
 
+# logger.debug("Table for TipRole/Tips relations")
 tiproles_tips = Table(
     "_tiproles_tips",
     Base.metadata,
@@ -78,6 +79,7 @@ tiproles_tips = Table(
     extend_existing=True
 )
 
+# logger.debug("Table for Process/TipRole relations")
 process_tiprole = Table(
     "_process_tiprole",
     Base.metadata,
@@ -86,6 +88,7 @@ process_tiprole = Table(
     extend_existing=True
 )
 
+# logger.debug("Table for Equipment/Tips relations")
 equipment_tips = Table(
     "_equipment_tips",
     Base.metadata,
@@ -410,6 +413,7 @@ class Reagent(BaseClass):
         except (TypeError, AttributeError) as e:
             place_holder = date.today()
             logger.error(f"We got a type error setting {self.lot} expiry: {e}. setting to today for testing")
+        # NOTE: The notation for not having an expiry is 1970.1.1
         if self.expiry.year == 1970:
             place_holder = "NA"
         else:
@@ -700,7 +704,13 @@ class SubmissionType(BaseClass):
             output[item.equipment_role.name] = emap
         return output
 
-    def construct_tips_map(self):
+    def construct_tips_map(self) -> dict:
+        """
+        Constructs map of tips to excel cells.
+
+        Returns:
+            dict: Tip locations in the excel sheet.
+        """        
         output = {}
         for item in self.submissiontype_tiprole_associations:
             tmap = item.uses
@@ -1142,6 +1152,7 @@ class Equipment(BaseClass):
                 processes = [process for process in processes if extraction_kit in process.kit_types]
             case _:
                 pass
+        # NOTE: Convert to strings
         processes = [process.name for process in processes]
         assert all([isinstance(process, str) for process in processes])
         if len(processes) == 0:
@@ -1193,7 +1204,8 @@ class Equipment(BaseClass):
         return cls.execute_query(query=query, limit=limit)
 
     def to_pydantic(self, submission_type: SubmissionType,
-                    extraction_kit: str | KitType | None = None) -> "PydEquipment":
+                    extraction_kit: str | KitType | None = None,
+                    role: str = None) -> "PydEquipment":
         """
         Creates PydEquipment of this Equipment
 
@@ -1206,7 +1218,7 @@ class Equipment(BaseClass):
         """
         from backend.validators.pydant import PydEquipment
         return PydEquipment(
-            processes=self.get_processes(submission_type=submission_type, extraction_kit=extraction_kit), role=None,
+            processes=self.get_processes(submission_type=submission_type, extraction_kit=extraction_kit), role=role,
             **self.to_dict(processes=False))
 
     @classmethod

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

@@ -17,7 +17,6 @@ orgs_contacts = Table(
     Base.metadata,
     Column("org_id", INTEGER, ForeignKey("_organization.id")),
     Column("contact_id", INTEGER, ForeignKey("_contact.id")),
-    # __table_args__ = {'extend_existing': True}
     extend_existing=True
 )
 

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

@@ -32,7 +32,7 @@ from pathlib import Path
 from jinja2.exceptions import TemplateNotFound
 from jinja2 import Template
 from docxtpl import InlineImage
-from io import BytesIO
+from docx.shared import Inches
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -229,6 +229,15 @@ class BasicSubmission(BaseClass):
 
     @classmethod
     def finalize_details(cls, input_dict: dict) -> dict:
+        """
+        Make final adjustments to the details dictionary before display.
+
+        Args:
+            input_dict (dict): Incoming dictionary.
+
+        Returns:
+            dict: Final details dictionary.
+        """        
         del input_dict['id']
         return input_dict
 
@@ -610,6 +619,12 @@ class BasicSubmission(BaseClass):
 
     @classmethod
     def get_regex(cls) -> str:
+        """
+        Dummy for inheritence.
+
+        Returns:
+            str: Regex for submission type.
+        """        
         return cls.construct_regex()
 
     # Polymorphic functions
@@ -733,7 +748,16 @@ class BasicSubmission(BaseClass):
 
     @classmethod
     def custom_docx_writer(cls, input_dict:dict, tpl_obj=None):
+        """
+        Adds custom fields to docx template writer for exported details.
 
+        Args:
+            input_dict (dict): Incoming default dictionary.
+            tpl_obj (_type_, optional): Template object. Defaults to None.
+
+        Returns:
+            dict: Dictionary with information added.
+        """        
         return input_dict
 
     @classmethod
@@ -785,6 +809,7 @@ class BasicSubmission(BaseClass):
             repeat = ""
         outstr = re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
         abb = cls.get_default_info('abbreviation')
+        outstr = re.sub(rf"RSL{abb}", rf"RSL-{abb}", outstr)
         return re.sub(rf"{abb}(\d)", rf"{abb}-\1", outstr)
 
     @classmethod
@@ -924,7 +949,7 @@ class BasicSubmission(BaseClass):
         if submission_type is not None:
             model = cls.find_polymorphic_subclass(polymorphic_identity=submission_type)
         elif len(kwargs) > 0:
-            # find the subclass containing the relevant attributes
+            # NOTE: find the subclass containing the relevant attributes
             # logger.debug(f"Attributes for search: {kwargs}")
             model = cls.find_polymorphic_subclass(attrs=kwargs)
         else:
@@ -1241,7 +1266,7 @@ class BacterialCulture(BasicSubmission):
             plate_map (dict | None, optional): _description_. Defaults to None.
 
         Returns:
-            dict: _description_
+            dict: Updated dictionary.
         """
         from . import ControlType
         input_dict = super().finalize_parse(input_dict, xl, info_map)
@@ -1495,7 +1520,17 @@ class Wastewater(BasicSubmission):
         # self.report.add_result(Result(msg=f"We added PCR info to {sub.rsl_plate_num}.", status='Information'))
 
     @classmethod
-    def custom_docx_writer(cls, input_dict:dict, tpl_obj=None):
+    def custom_docx_writer(cls, input_dict:dict, tpl_obj=None) -> dict:
+        """
+        Adds custom fields to docx template writer for exported details. Extends parent.
+
+        Args:
+            input_dict (dict): Incoming default dictionary.
+            tpl_obj (_type_, optional): Template object. Defaults to None.
+
+        Returns:
+            dict: Dictionary with information added.
+        """        
         from backend.excel.writer import DocxWriter
         input_dict = super().custom_docx_writer(input_dict)
         well_24 = []
@@ -1611,6 +1646,7 @@ class WastewaterArtic(BasicSubmission):
         instr = re.sub(r"^(\d{6})", f"RSL-AR-\\1", instr)
         # logger.debug(f"name coming out of Artic namer: {instr}")
         outstr = super().enforce_name(instr=instr, data=data)
+        outstr = outstr.replace("RSLAR", "RSL-AR")
         return outstr
 
     @classmethod
@@ -1788,7 +1824,6 @@ class WastewaterArtic(BasicSubmission):
         input_excel = super().custom_info_writer(input_excel, info, backup)
         # logger.debug(f"Info:\n{pformat(info)}")
         # NOTE: check for source plate information
-        # check = 'source_plates' in info.keys() and info['source_plates'] is not None
         if check_key_or_attr(key='source_plates', interest=info, check_none=True):
             worksheet = input_excel['First Strand List']
             start_row = 8
@@ -1805,15 +1840,11 @@ class WastewaterArtic(BasicSubmission):
                 except TypeError:
                     pass
         # NOTE: check for gel information
-        # check = 'gel_info' in info.keys() and info['gel_info']['value'] is not None
         if check_key_or_attr(key='gel_info', interest=info, check_none=True):
             # logger.debug(f"Gel info check passed.")
-            # if info['gel_info'] is not None:
-            # logger.debug(f"Gel info not none.")
             # NOTE: print json field gel results to Egel results
             worksheet = input_excel['Egel results']
             # TODO: Move all this into a seperate function?
-            #
             start_row = 21
             start_column = 15
             for row, ki in enumerate(info['gel_info']['value'], start=1):
@@ -1831,13 +1862,11 @@ class WastewaterArtic(BasicSubmission):
                         worksheet.cell(row=row, column=column, value=kj['value'])
                     except AttributeError:
                         logger.error(f"Failed {kj['name']} with value {kj['value']} to row {row}, column {column}")
-        # check = 'gel_image' in info.keys() and info['gel_image']['value'] is not None
+        if check_key_or_attr(key='gel_image_path', interest=info, check_none=True):
-        if check_key_or_attr(key='gel_image', interest=info, check_none=True):
-            # if info['gel_image'] is not None:
             worksheet = input_excel['Egel results']
             # logger.debug(f"We got an image: {info['gel_image']}")
             with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
-                z = zipped.extract(info['gel_image']['value'], Path(TemporaryDirectory().name))
+                z = zipped.extract(info['gel_image_path']['value'], Path(TemporaryDirectory().name))
                 img = OpenpyxlImage(z)
                 img.height = 400  # insert image height in pixels as float or int (e.g. 305.5)
                 img.width = 600
@@ -1860,36 +1889,16 @@ class WastewaterArtic(BasicSubmission):
         base_dict['excluded'] += ['gel_info', 'gel_image', 'headers', "dna_core_submission_number", "source_plates",
                                   "gel_controls, gel_image_path"]
         base_dict['DNA Core ID'] = base_dict['dna_core_submission_number']
-        # check = 'gel_info' in base_dict.keys() and base_dict['gel_info'] is not None
         if check_key_or_attr(key='gel_info', interest=base_dict, check_none=True):
             headers = [item['name'] for item in base_dict['gel_info'][0]['values']]
             base_dict['headers'] = [''] * (4 - len(headers))
             base_dict['headers'] += headers
             # logger.debug(f"Gel info: {pformat(base_dict['headers'])}")
-        # check = 'gel_image' in base_dict.keys() and base_dict['gel_image'] is not None
         if check_key_or_attr(key='gel_image_path', interest=base_dict, check_none=True):
             with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
                 base_dict['gel_image'] = base64.b64encode(zipped.read(base_dict['gel_image_path'])).decode('utf-8')
         return base_dict, template
 
-    # def adjust_to_dict_samples(self, backup: bool = False) -> List[dict]:
-    #     """
-    #     Updates sample dictionaries with custom values
-    #
-    #     Args:
-    #         backup (bool, optional): Whether to perform backup. Defaults to False.
-    #
-    #     Returns:
-    #         List[dict]: Updated dictionaries
-    #     """
-    #     # logger.debug(f"Hello from {self.__class__.__name__} dictionary sample adjuster.")
-    #     output = []
-    #
-    #     for assoc in self.submission_sample_associations:
-    #         dicto = assoc.to_sub_dict()
-    #         output.append(dicto)
-    #     return output
-
     def custom_context_events(self) -> dict:
         """
         Creates dictionary of str:function to be passed to context menu. Extends parent
@@ -1902,6 +1911,13 @@ class WastewaterArtic(BasicSubmission):
         return events
 
     def set_attribute(self, key: str, value):
+        """
+        Performs custom attribute setting based on values. Extends parent
+
+        Args:
+            key (str): name of attribute
+            value (_type_): value of attribute
+        """
         super().set_attribute(key=key, value=value)
         if key == 'gel_info':
             if len(self.gel_info) > 3:
@@ -1938,7 +1954,17 @@ class WastewaterArtic(BasicSubmission):
             self.save()
 
     @classmethod
-    def custom_docx_writer(cls, input_dict:dict, tpl_obj=None):
+    def custom_docx_writer(cls, input_dict:dict, tpl_obj=None) -> dict:
+        """
+        Adds custom fields to docx template writer for exported details.
+
+        Args:
+            input_dict (dict): Incoming default dictionary/
+            tpl_obj (_type_, optional): Template object. Defaults to None.
+
+        Returns:
+            dict: Dictionary with information added.
+        """        
         input_dict = super().custom_docx_writer(input_dict)
         if check_key_or_attr(key='gel_image_path', interest=input_dict, check_none=True):
             with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
@@ -1946,12 +1972,11 @@ class WastewaterArtic(BasicSubmission):
             with tempfile.TemporaryFile(mode="wb", suffix=".jpg", delete=False) as tmp:
                 tmp.write(img)
             logger.debug(f"Tempfile: {tmp.name}")
-        img = InlineImage(tpl_obj, image_descriptor=tmp.name)#, width=5.5)#, height=400)
+        img = InlineImage(tpl_obj, image_descriptor=tmp.name, width=Inches(5.5))#, width=5.5)#, height=400)
         input_dict['gel_image'] = img
         return input_dict
 
 
-
 # Sample Classes
 
 class BasicSample(BaseClass):
@@ -2009,6 +2034,12 @@ class BasicSample(BaseClass):
 
     @classmethod
     def timestamps(cls) -> List[str]:
+        """
+        Constructs a list of all attributes stored as SQL Timestamps
+
+        Returns:
+            List[str]: Attribute list
+        """        
         output = [item.name for item in cls.__table__.columns if isinstance(item.type, TIMESTAMP)]
         if issubclass(cls, BasicSample) and not cls.__name__ == "BasicSample":
             output += BasicSample.timestamps()
@@ -2082,10 +2113,6 @@ class BasicSample(BaseClass):
         logger.info(f"Recruiting model: {model}")
         return model
 
-    @classmethod
-    def sql_enforcer(cls, pyd_sample: "PydSample"):
-        return pyd_sample
-
     @classmethod
     def parse_sample(cls, input_dict: dict) -> dict:
         f"""
@@ -2194,6 +2221,15 @@ class BasicSample(BaseClass):
                      # limit: int = 0,
                      **kwargs
                      ) -> List[BasicSample]:
+        """
+        Allows for fuzzy search of samples. (Experimental)
+
+        Args:
+            sample_type (str | BasicSample | None, optional): Type of sample. Defaults to None.
+
+        Returns:
+            List[BasicSample]: List of samples that match kwarg search parameters.
+        """                     
         match sample_type:
             case str():
                 model = cls.find_polymorphic_subclass(polymorphic_identity=sample_type)
@@ -2220,26 +2256,20 @@ class BasicSample(BaseClass):
         return [dict(label="Submitter ID", field="submitter_id")]
 
     @classmethod
-    def samples_to_df(cls, sample_type: str | None | BasicSample = None, **kwargs):
+    def samples_to_df(cls, sample_list:List[BasicSample], **kwargs) -> pd.DataFrame:
-        # def samples_to_df(cls, sample_type:str|None|BasicSample=None, searchables:dict={}):
+        """
-        logger.debug(f"Checking {sample_type} with type {type(sample_type)}")
+        Runs a fuzzy search and converts into a dataframe.
-        match sample_type:
+
-            case str():
+        Args:
-                model = BasicSample.find_polymorphic_subclass(polymorphic_identity=sample_type)
+            sample_list (List[BasicSample]): List of samples to be parsed. Defaults to None.
-            case _:
+
-                try:
+        Returns:
-                    check = issubclass(sample_type, BasicSample)
+            pd.DataFrame: Dataframe all samples
-                except TypeError:
+        """
-                    check = False
+        if not isinstance(sample_list, list):
-                if check:
+            sample_list = [sample_list]
-                    model = sample_type
-                else:
-                    model = cls
-        q_out = model.fuzzy_search(sample_type=sample_type, **kwargs)
-        if not isinstance(q_out, list):
-            q_out = [q_out]
         try:
-            samples = [sample.to_sub_dict() for sample in q_out]
+            samples = [sample.to_sub_dict() for sample in sample_list]
         except TypeError as e:
             logger.error(f"Couldn't find any samples with data: {kwargs}\nDue to {e}")
             return None
@@ -2287,6 +2317,12 @@ class WastewaterSample(BasicSample):
 
     @classmethod
     def get_default_info(cls, *args):
+        """
+        Returns default info for a model. Extends BaseClass method.
+
+        Returns:
+            dict | list | str: Output of key:value dict or single (list, str) desired variable
+        """        
         dicto = super().get_default_info(*args)
         match dicto:
             case dict():

src/submissions/backend/validators/pydant.py

@@ -740,7 +740,10 @@ class PydSubmission(BaseModel, extra='allow'):
                         if tips is None:
                             continue
                         logger.debug(f"Converting tips: {tips} to sql.")
-                        association = tips.to_sql(submission=instance)
+                        try:
+                            association = tips.to_sql(submission=instance)
+                        except AttributeError:
+                            continue
                         if association is not None and association not in instance.submission_tips_associations:
                             # association.save()
                             instance.submission_tips_associations.append(association)

src/submissions/frontend/widgets/equipment_usage.py

@@ -99,6 +99,7 @@ class RoleComboBox(QWidget):
             self.check.setChecked(False)
         else:
             self.check.setChecked(True)
+        self.check.stateChanged.connect(self.toggle_checked)
         self.box = QComboBox()
         self.box.setMaximumWidth(200)
         self.box.setMinimumWidth(200)
@@ -118,6 +119,7 @@ class RoleComboBox(QWidget):
         self.layout.addWidget(self.box, 0, 2)
         self.layout.addWidget(self.process, 0, 3)
         self.setLayout(self.layout)
+        self.toggle_checked()
 
     def update_processes(self):
         """
@@ -176,3 +178,14 @@ class RoleComboBox(QWidget):
             )
         except Exception as e:
             logger.error(f"Could create PydEquipment due to: {e}")
+
+    def toggle_checked(self):
+        for widget in self.findChildren(QWidget):
+            match widget:
+                case QCheckBox():
+                    continue
+                case _:
+                    if self.check.isChecked():
+                        widget.setEnabled(True)
+                    else:
+                        widget.setEnabled(False)

src/submissions/frontend/widgets/sample_search.py

@@ -51,7 +51,9 @@ class SearchBox(QDialog):
 
     def update_data(self):
         fields = self.parse_form()
-        data = self.type.samples_to_df(sample_type=self.type, **fields)
+        # data = self.type.samples_to_df(sample_type=self.type, **fields)
+        data = self.type.fuzzy_search(sample_type=self.type, **fields)
+        data = self.type.samples_to_df(sample_list=data)
         # logger.debug(f"Data: {data}")
         self.results.setData(df=data)
 

src/submissions/frontend/widgets/submission_details.py

@@ -20,8 +20,6 @@ from PIL import Image
 from typing import List
 from backend.excel.writer import DocxWriter
 
-
-
 logger = logging.getLogger(f"submissions.{__name__}")
 
 
@@ -97,7 +95,7 @@ class SubmissionDetails(QDialog):
         template_path = Path(self.template.environment.loader.__getattribute__("searchpath")[0])
         with open(template_path.joinpath("css", "styles.css"), "r") as f:
             css = f.read()
-        logger.debug(f"Submission_details: {pformat(self.base_dict)}")
+        # logger.debug(f"Submission_details: {pformat(self.base_dict)}")
         self.html = self.template.render(sub=self.base_dict, signing_permission=is_power_user(), css=css)
         self.webview.setHtml(self.html)
         self.setWindowTitle(f"Submission Details - {submission.rsl_plate_num}")
@@ -118,30 +116,10 @@ class SubmissionDetails(QDialog):
         writer = DocxWriter(base_dict=self.base_dict)
         fname = select_save_file(obj=self, default_name=self.base_dict['plate_number'], extension="docx")
         writer.save(fname)
-        # image_io = BytesIO()
-        # temp_dir = Path(TemporaryDirectory().name)
-        # hti = Html2Image(output_path=temp_dir, size=(2400, 1500))
-        # temp_file = Path(TemporaryFile(dir=temp_dir, suffix=".png").name)
-        # screenshot = hti.screenshot(self.base_dict['platemap'], save_as=temp_file.name)
-        # export_map = Image.open(screenshot[0])
-        # export_map = export_map.convert('RGB')
-        # try:
-        #     export_map.save(image_io, 'JPEG')
-        # except AttributeError:
-        #     logger.error(f"No plate map found")
-        # self.base_dict['export_map'] = base64.b64encode(image_io.getvalue()).decode('utf-8')
-        # del self.base_dict['platemap']
-        # self.html2 = self.template.render(sub=self.base_dict)
         try:
             html_to_pdf(html=self.html, output_file=fname)
         except PermissionError as e:
             logger.error(f"Error saving pdf: {e}")
-        #     msg = QMessageBox()
-        #     msg.setText("Permission Error")
-        #     msg.setInformativeText(f"Looks like {fname.__str__()} is open.\nPlease close it and try again.")
-        #     msg.setWindowTitle("Permission Error")
-        #     msg.exec()
-
 
 class SubmissionComment(QDialog):
     """