Replaced some list comprehension with generators, javascript in templates to create click event.

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

@@ -283,6 +283,17 @@ class BasicSubmission(BaseClass):
         del input_dict['id']
         return input_dict
 
+    def generate_associations(self, name:str, extra:str|None=None):
+        try:
+            field = self.__getattribute__(name)
+        except AttributeError:
+            return None
+        for item in field:
+            if extra:
+                yield item.to_sub_dict(extra)
+            else:
+                yield item.to_sub_dict()
+
     def to_dict(self, full_data: bool = False, backup: bool = False, report: bool = False) -> dict:
         """
         Constructs dictionary used in submissions summary
@@ -332,6 +343,10 @@ class BasicSubmission(BaseClass):
             try:
                 reagents = [item.to_sub_dict(extraction_kit=self.extraction_kit) for item in
                             self.submission_reagent_associations]
+            except Exception as e:
+                logger.error(f"We got an error retrieving reagents: {e}")
+                reagents = []
+            finally:
                 for k, v in self.extraction_kit.construct_xl_map_for_use(self.submission_type):
                     if k == 'info':
                         continue
@@ -341,26 +356,26 @@ class BasicSubmission(BaseClass):
                         reagents.append(
                             dict(role=k, name="Not Applicable", lot="NA", expiry=expiry,
                                  missing=True))
-            except Exception as e:
-                logger.error(f"We got an error retrieving reagents: {e}")
-                reagents = None
             # logger.debug(f"Running samples.")
-            samples = self.adjust_to_dict_samples(backup=backup)
+            # samples = self.adjust_to_dict_samples(backup=backup)
+            samples = self.generate_associations(name="submission_sample_associations")
             # logger.debug("Running equipment")
-            try:
+            equipment = self.generate_associations(name="submission_equipment_associations")
-                equipment = [item.to_sub_dict() for item in self.submission_equipment_associations]
+            # try:
-                if not equipment:
+            #     equipment = [item.to_sub_dict() for item in self.submission_equipment_associations]
-                    equipment = None
+            #     if not equipment:
-            except Exception as e:
+            #         equipment = None
-                logger.error(f"Error setting equipment: {e}")
+            # except Exception as e:
-                equipment = None
+            #     logger.error(f"Error setting equipment: {e}")
-            try:
+            #     equipment = None
-                tips = [item.to_sub_dict() for item in self.submission_tips_associations]
+            tips = self.generate_associations(name="submission_tips_associations")
-                if not tips:
+            # try:
-                    tips = None
+            #     tips = [item.to_sub_dict() for item in self.submission_tips_associations]
-            except Exception as e:
+            #     if not tips:
-                logger.error(f"Error setting tips: {e}")
+            #         tips = None
-                tips = None
+            # except Exception as e:
+            #     logger.error(f"Error setting tips: {e}")
+            #     tips = None
             cost_centre = self.cost_centre
             custom = self.custom
         else:
@@ -1013,18 +1028,18 @@ class BasicSubmission(BaseClass):
         logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} sampler")
         return samples
 
-    def adjust_to_dict_samples(self, backup: bool = False) -> List[dict]:
+    # def adjust_to_dict_samples(self, backup: bool = False) -> List[dict]:
-        """
+    #     """
-        Updates sample dictionaries with custom values
+    #     Updates sample dictionaries with custom values
-
+    #
-        Args:
+    #     Args:
-            backup (bool, optional): Whether to perform backup. Defaults to False.
+    #         backup (bool, optional): Whether to perform backup. Defaults to False.
-
+    #
-        Returns:
+    #     Returns:
-            List[dict]: Updated dictionaries
+    #         List[dict]: Updated dictionaries
-        """
+    #     """
-        # logger.debug(f"Hello from {self.__class__.__name__} dictionary sample adjuster.")
+    #     # logger.debug(f"Hello from {self.__class__.__name__} dictionary sample adjuster.")
-        return [item.to_sub_dict() for item in self.submission_sample_associations]
+    #     return [item.to_sub_dict() for item in self.submission_sample_associations]
 
     @classmethod
     def get_details_template(cls, base_dict: dict) -> Tuple[dict, Template]:

src/submissions/backend/excel/parser.py

@@ -53,7 +53,6 @@ class SheetParser(object):
         self.parse_samples()
         self.parse_equipment()
         self.parse_tips()
-        # self.finalize_parse()
         # logger.debug(f"Parser.sub after info scrape: {pformat(self.sub)}")
 
     def parse_info(self):
@@ -63,6 +62,8 @@ class SheetParser(object):
         parser = InfoParser(xl=self.xl, submission_type=self.submission_type, sub_object=self.sub_object)
         info = parser.parse_info()
         self.info_map = parser.map
+        # NOTE: in order to accommodate generic submission types we have to check for the type in the excel sheet and
+        # rerun accordingly
         try:
             check = info['submission_type']['value'] not in [None, "None", "", " "]
         except KeyError:
@@ -78,13 +79,15 @@ class SheetParser(object):
             else:
                 self.submission_type = RSLNamer.retrieve_submission_type(filename=self.filepath)
                 self.parse_info()
-        for k, v in info.items():
+        [self.sub.__setitem__(k, v) for k, v in info.items()]
-            match k:
+        # for k, v in info.items():
-                # NOTE: exclude samples.
+        #     match k:
-                case "sample":
+        #         # NOTE: exclude samples.
-                    continue
+        #         case "sample":
-                case _:
+        #             logger.debug(f"Sample found: {k}: {v}")
-                    self.sub[k] = v
+        #             continue
+        #         case _:
+        #             self.sub[k] = v
 
     def parse_reagents(self, extraction_kit: str | None = None):
         """
@@ -105,7 +108,7 @@ class SheetParser(object):
         Calls sample parser to pull info from the excel sheet
         """
         parser = SampleParser(xl=self.xl, submission_type=self.submission_type)
-        self.sub['samples'] = parser.reconcile_samples()
+        self.sub['samples'] = parser.parse_samples()
 
     def parse_equipment(self):
         """
@@ -145,29 +148,29 @@ class SheetParser(object):
             PydSubmission: output pydantic model
         """
         # logger.debug(f"Submission dictionary coming into 'to_pydantic':\n{pformat(self.sub)}")
-        pyd_dict = copy(self.sub)
+        # pyd_dict = copy(self.sub)
-        pyd_dict['samples'] = [PydSample(**sample) for sample in self.sub['samples']]
+        # self.sub['samples'] = [PydSample(**sample) for sample in self.sub['samples']]
         # logger.debug(f"Reagents: {pformat(self.sub['reagents'])}")
-        pyd_dict['reagents'] = [PydReagent(**reagent) for reagent in self.sub['reagents']]
+        # self.sub['reagents'] = [PydReagent(**reagent) for reagent in self.sub['reagents']]
         # logger.debug(f"Equipment: {self.sub['equipment']}")
-        try:
+        # try:
-            check = bool(self.sub['equipment'])
+        #     check = bool(self.sub['equipment'])
-        except TypeError:
+        # except TypeError:
-            check = False
+        #     check = False
-        if check:
+        # if check:
-            pyd_dict['equipment'] = [PydEquipment(**equipment) for equipment in self.sub['equipment']]
+        #     self.sub['equipment'] = [PydEquipment(**equipment) for equipment in self.sub['equipment']]
-        else:
+        # else:
-            pyd_dict['equipment'] = None
+        #     self.sub['equipment'] = None
-        try:
+        # try:
-            check = bool(self.sub['tips'])
+        #     check = bool(self.sub['tips'])
-        except TypeError:
+        # except TypeError:
-            check = False
+        #     check = False
-        if check:
+        # if check:
-            pyd_dict['tips'] = [PydTips(**tips) for tips in self.sub['tips']]
+        #     self.sub['tips'] = [PydTips(**tips) for tips in self.sub['tips']]
-        else:
+        # else:
-            pyd_dict['tips'] = None
+        #     self.sub['tips'] = None
-        psm = PydSubmission(filepath=self.filepath, run_custom=True, **pyd_dict)
+        return PydSubmission(filepath=self.filepath, run_custom=True, **self.sub)
-        return psm
+        # return psm
 
 
 class InfoParser(object):
@@ -287,7 +290,7 @@ class ReagentParser(object):
             extraction_kit (str): Extraction kit used.
             sub_object (BasicSubmission | None, optional): Submission object holding methods. Defaults to None.
         """
-        # logger.debug("\n\nHello from ReagentParser!\n\n")
+        logger.debug("\n\nHello from ReagentParser!\n\n")
         if isinstance(submission_type, str):
             submission_type = SubmissionType.query(name=submission_type)
         self.submission_type_obj = submission_type
@@ -382,7 +385,7 @@ class SampleParser(object):
             sample_map (dict | None, optional): Locations in database where samples are found. Defaults to None.
             sub_object (BasicSubmission | None, optional): Submission object holding methods. Defaults to None.
         """
-        # logger.debug("\n\nHello from SampleParser!\n\n")
+        logger.debug("\n\nHello from SampleParser!\n\n")
         self.samples = []
         self.xl = xl
         if isinstance(submission_type, str):
@@ -477,49 +480,50 @@ class SampleParser(object):
                 lookup_samples.append(self.samp_object.parse_sample(row_dict))
         return lookup_samples
 
-    def parse_samples(self) -> Tuple[Report | None, List[dict] | List[PydSample]]:
+    # def parse_samples(self) -> Tuple[Report | None, List[dict] | List[PydSample]]:
-        """
+    #     """
-        Parse merged platemap/lookup info into dicts/samples
+    #     Parse merged platemap/lookup info into dicts/samples
+    #
+    #     Returns:
+    #         List[dict]|List[models.BasicSample]: List of samples
+    #     """
+    #     result = None
+    #     new_samples = []
+    #     # logger.debug(f"Starting samples: {pformat(self.samples)}")
+    #     for sample in self.samples:
+    #         translated_dict = {}
+    #         for k, v in sample.items():
+    #             match v:
+    #                 case dict():
+    #                     v = None
+    #                 case float():
+    #                     v = convert_nans_to_nones(v)
+    #                 case _:
+    #                     v = v
+    #             translated_dict[k] = convert_nans_to_nones(v)
+    #         translated_dict['sample_type'] = f"{self.submission_type} Sample"
+    #         translated_dict = self.sub_object.parse_samples(translated_dict)
+    #         translated_dict = self.samp_object.parse_sample(translated_dict)
+    #         # logger.debug(f"Here is the output of the custom parser:\n{translated_dict}")
+    #         new_samples.append(PydSample(**translated_dict))
+    #     return result, new_samples
 
-        Returns:
+    def parse_samples(self) -> Generator[dict, None, None]:
-            List[dict]|List[models.BasicSample]: List of samples
-        """
-        result = None
-        new_samples = []
-        # logger.debug(f"Starting samples: {pformat(self.samples)}")
-        for sample in self.samples:
-            translated_dict = {}
-            for k, v in sample.items():
-                match v:
-                    case dict():
-                        v = None
-                    case float():
-                        v = convert_nans_to_nones(v)
-                    case _:
-                        v = v
-                translated_dict[k] = convert_nans_to_nones(v)
-            translated_dict['sample_type'] = f"{self.submission_type} Sample"
-            translated_dict = self.sub_object.parse_samples(translated_dict)
-            translated_dict = self.samp_object.parse_sample(translated_dict)
-            # logger.debug(f"Here is the output of the custom parser:\n{translated_dict}")
-            new_samples.append(PydSample(**translated_dict))
-        return result, new_samples
-
-    def reconcile_samples(self) -> Generator[dict, None, None]:
         """
         Merges sample info from lookup table and plate map.
 
         Returns:
             List[dict]: Reconciled samples
         """
-        if self.plate_map_samples is None or self.lookup_samples is None:
+        if not self.plate_map_samples or not self.lookup_samples:
+            logger.error(f"No separate samples, returning")
             self.samples = self.lookup_samples or self.plate_map_samples
             return
         merge_on_id = self.sample_info_map['lookup_table']['merge_on_id']
         plate_map_samples = sorted(copy(self.plate_map_samples), key=lambda d: d['id'])
         lookup_samples = sorted(copy(self.lookup_samples), key=lambda d: d[merge_on_id])
-        print(pformat(plate_map_samples))
+        # print(pformat(plate_map_samples))
-        print(pformat(lookup_samples))
+        # print(pformat(lookup_samples))
         for ii, psample in enumerate(plate_map_samples):
             try:
                 check = psample['id'] == lookup_samples[ii][merge_on_id]
@@ -563,6 +567,7 @@ class EquipmentParser(object):
             xl (Workbook): Openpyxl workbook from submitted excel file.
             submission_type (str | SubmissionType): Type of submission expected (Wastewater, Bacterial Culture, etc.)
         """
+        logger.debug("\n\nHello from EquipmentParser!\n\n")
         if isinstance(submission_type, str):
             submission_type = SubmissionType.query(name=submission_type)
         self.submission_type = submission_type
@@ -649,6 +654,7 @@ class TipParser(object):
             xl (Workbook): Openpyxl workbook from submitted excel file.
             submission_type (str | SubmissionType): Type of submission expected (Wastewater, Bacterial Culture, etc.)
         """
+        logger.debug("\n\nHello from TipParser!\n\n")
         if isinstance(submission_type, str):
             submission_type = SubmissionType.query(name=submission_type)
         self.submission_type = submission_type

src/submissions/backend/validators/pydant.py

@@ -9,6 +9,7 @@ from datetime import date, datetime, timedelta
 from dateutil.parser import parse
 from dateutil.parser import ParserError
 from typing import List, Tuple, Literal
+from types import GeneratorType
 from . import RSLNamer
 from pathlib import Path
 from tools import check_not_nan, convert_nans_to_nones, Report, Result
@@ -395,16 +396,32 @@ class PydSubmission(BaseModel, extra='allow'):
     submission_category: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
     comment: dict | None = Field(default=dict(value="", missing=True), validate_default=True)
     reagents: List[dict] | List[PydReagent] = []
-    samples: List[PydSample]
+    samples: List[PydSample] | Generator
     equipment: List[PydEquipment] | None = []
     cost_centre: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
     contact: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
+    tips: List[PydTips] | None =[]
+
+    @field_validator("tips", mode="before")
+    @classmethod
+    def expand_tips(cls, value):
+        # print(f"\n{type(value)}\n")
+        if isinstance(value, dict):
+            value = value['value']
+        if isinstance(value, Generator):
+            logger.debug("We have a generator")
+            return [PydTips(**tips) for tips in value]
+        if not value:
+            return []
+        return value
 
     @field_validator('equipment', mode='before')
     @classmethod
     def convert_equipment_dict(cls, value):
         # logger.debug(f"Equipment: {value}")
-
+        if isinstance(value, Generator):
+            logger.debug("We have a generator")
+            return [PydEquipment(**equipment) for equipment in value]
         if isinstance(value, dict):
             return value['value']
         return value
@@ -580,6 +597,24 @@ class PydSubmission(BaseModel, extra='allow'):
             value['value'] = values.data['submission_type']['value']
         return value
 
+    @field_validator("reagents", mode="before")
+    @classmethod
+    def expand_reagents(cls, value):
+        # print(f"\n{type(value)}\n")
+        if isinstance(value, Generator):
+            logger.debug("We have a generator")
+            return [PydReagent(**reagent) for reagent in value]
+        return value
+
+    @field_validator("samples", mode="before")
+    @classmethod
+    def expand_samples(cls, value):
+        # print(f"\n{type(value)}\n")
+        if isinstance(value, Generator):
+            logger.debug("We have a generator")
+            return [PydSample(**sample) for sample in value]
+        return value
+
     @field_validator("samples")
     @classmethod
     def assign_ids(cls, value):

src/submissions/frontend/widgets/submission_details.py

@@ -93,15 +93,16 @@ class SubmissionDetails(QDialog):
         Args:
             sample (str): Submitter Id of the sample.
         """
+        logger.debug(f"Details: {sample}")
         if isinstance(sample, str):
             sample = BasicSample.query(submitter_id=sample)
         base_dict = sample.to_sub_dict(full_data=True)
         exclude = ['submissions', 'excluded', 'colour', 'tooltip']
-        try:
+        # try:
-            base_dict['excluded'] += exclude
+        #     base_dict['excluded'] += exclude
-        except KeyError:
+        # except KeyError:
-            base_dict['excluded'] = exclude
+        base_dict['excluded'] = exclude
-        template = sample.get_details_template(base_dict=base_dict)
+        template = sample.get_details_template()
         template_path = Path(self.template.environment.loader.__getattribute__("searchpath")[0])
         with open(template_path.joinpath("css", "styles.css"), "r") as f:
             css = f.read()
@@ -158,6 +159,8 @@ class SubmissionDetails(QDialog):
         # logger.debug(f"Submission_details: {pformat(self.base_dict)}")
         # logger.debug(f"User is power user: {is_power_user()}")
         self.html = self.template.render(sub=self.base_dict, signing_permission=is_power_user(), css=css)
+        with open("test.html", "w") as f:
+            f.write(self.html)
         self.webview.setHtml(self.html)
 
 

src/submissions/templates/basicsubmission_details.html

@@ -20,7 +20,7 @@
 
         <h3><u>Reagents:</u></h3>
         <p>{% for item in sub['reagents'] %}
-            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['role'] }}</b>: <a class="data-link" id="{{ item['lot'] }}">{{ item['lot'] }} (EXP: {{ item['expiry'] }})</a><br>
+            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['role'] }}</b>: <a class="data-link reagent" id="{{ item['lot'] }}">{{ item['lot'] }} (EXP: {{ item['expiry'] }})</a><br>
         {% endfor %}</p>
 
         {% if sub['equipment'] %}
@@ -38,7 +38,7 @@
         {% if sub['samples'] %}
         <h3><u>Samples:</u></h3>
         <p>{% for item in sub['samples'] %}
-            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['well'] }}:</b><a class="data-link" id="{{ item['submitter_id'] }}_alpha">{% if item['organism'] %} {{ item['name'] }} - ({{ item['organism']|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}){% else %} {{ item['name']|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}{% endif %}</a><br>
+            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['well'] }}:</b><a class="data-link sample" id="{{ item['submitter_id'] }}">{% if item['organism'] %} {{ item['name'] }} - ({{ item['organism']|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}){% else %} {{ item['name']|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}{% endif %}</a><br>
         {% endfor %}</p>
         {% endif %}
 
@@ -83,22 +83,25 @@
     <script>
         {% block script %}
         {{ super() }}
-        {% for sample in sub['samples'] %}
+
-        document.getElementById("{{ sample['submitter_id'] }}").addEventListener("click", function(){
-            backend.sample_details("{{ sample['submitter_id'] }}");
-        });
-        document.getElementById("{{ sample['submitter_id'] }}_alpha").addEventListener("click", function(){
-            backend.sample_details("{{ sample['submitter_id'] }}");
-        });
-        {% endfor %}
-        {% for reagent in sub['reagents'] %}
-        document.getElementById("{{ reagent['lot'] }}").addEventListener("click", function(){
-            backend.reagent_details("{{ reagent['lot'] }}", "{{ sub['extraction_kit'] }}");
-        });
-        {% endfor %}
         document.getElementById("sign_btn").addEventListener("click", function(){
             backend.sign_off("{{ sub['plate_number'] }}");
         });
+        var sampleSelection = document.getElementsByClassName('sample');
+
+        for(let i = 0; i < sampleSelection.length; i++) {
+          sampleSelection[i].addEventListener("click", function() {
+            backend.sample_details(sampleSelection[i].id);
+          })
+        }
+
+        var reagentSelection = document.getElementsByClassName('reagent');
+
+        for(let i = 0; i < reagentSelection.length; i++) {
+          reagentSelection[i].addEventListener("click", function() {
+            backend.reagent_details(reagentSelection[i].id, "{{ sub['extraction_kit'] }}");
+          })
+        }
 
         {% endblock %}
     </script>

src/submissions/templates/plate_map.html

@@ -1,6 +1,6 @@
         <div class="gallery" style="display: grid;grid-template-columns: repeat({{ PLATE_COLUMNS }}, 7.5vw);grid-template-rows: repeat({{ PLATE_ROWS }}, 7.5vw);grid-gap: 2px;">
             {% for sample in samples %}
-                <div class="well data-link" id="{{sample['submitter_id']}}" style="background-color: {{sample['background_color']}};
+                <div class="well data-link sample" id="{{sample['submitter_id']}}" style="background-color: {{sample['background_color']}};
                 border: 1px solid #000;
                 padding: 20px;
                 grid-column-start: {{sample['column']}};