Ui interface updates.

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

@@ -13,6 +13,7 @@ from sqlalchemy import Column, INTEGER, String, JSON
 from sqlalchemy.ext.associationproxy import AssociationProxy
 from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session, InstrumentedAttribute, ColumnProperty
 from sqlalchemy.ext.declarative import declared_attr
+from sqlalchemy.ext.hybrid import hybrid_property
 from sqlalchemy.exc import ArgumentError
 from typing import Any, List, ClassVar
 from pathlib import Path
@@ -237,10 +238,10 @@ class BaseClass(Base):
     @classmethod
     def query_or_create(cls, **kwargs) -> Tuple[Any, bool]:
         new = False
-        allowed = [k for k, v in cls.__dict__.items() if isinstance(v, InstrumentedAttribute)]
+        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}
-        # logger.debug(f"Sanitized kwargs: {sanitized_kwargs}")
+        logger.debug(f"Sanitized kwargs: {sanitized_kwargs}")
         instance = cls.query(**sanitized_kwargs)
         if not instance or isinstance(instance, list):
             instance = cls()
@@ -273,7 +274,7 @@ class BaseClass(Base):
         return cls.execute_query(**kwargs)
 
     @classmethod
-    def execute_query(cls, query: Query = None, model=None, limit: int = 0, **kwargs) -> Any | List[Any]:
+    def execute_query(cls, query: Query = None, model=None, limit: int = 0, offset:int|None=None, **kwargs) -> Any | List[Any]:
         """
         Execute sqlalchemy query with relevant defaults.
 
@@ -291,22 +292,32 @@ class BaseClass(Base):
         # logger.debug(f"Model: {model}")
         if query is None:
             query: Query = cls.__database_session__.query(cls)
+        else:
+            logger.debug(f"Incoming query: {query}")
         singles = cls.get_default_info('singles')
         for k, v in kwargs.items():
-
+            logger.info(f"Using key: {k} with value: {v} against {cls}")
-            logger.info(f"Using key: {k} with value: {v}")
             try:
                 attr = getattr(cls, k)
-                # NOTE: account for attrs that use list.
-                if attr.property.uselist:
-                    query = query.filter(attr.contains(v))
-                else:
-                    query = query.filter(attr == v)
             except (ArgumentError, AttributeError) as e:
-                logger.error(f"Attribute {k} unavailable due to:\n\t{e}\nSkipping.")
+                logger.error(f"Attribute {k} unavailable due to:\n\t{e}\n.")
+                continue
+                # NOTE: account for attrs that use list.
+            try:
+                check = attr.property.uselist
+            except AttributeError:
+                check = False
+            if check:
+                logger.debug("Got uselist")
+                query = query.filter(attr.contains(v))
+            else:
+                logger.debug("Single item.")
+                query = query.filter(attr == v)
             if k in singles:
                 logger.warning(f"{k} is in singles. Returning only one value.")
                 limit = 1
+        if offset:
+            query.offset(offset)
         with query.session.no_autoflush:
             match limit:
                 case 0:
@@ -476,13 +487,13 @@ class BaseClass(Base):
         # logger.debug(f"Attempting to set: {key} to {value}")
         if key.startswith("_"):
             return super().__setattr__(key, value)
-        try:
+        # try:
-            check = not hasattr(self, key)
+        check = not hasattr(self, key)
-        except:
+        # except:
-            return
+        #     return
         if check:
             try:
-                json.dumps(value)
+                value = json.dumps(value)
             except TypeError:
                 value = str(value)
             self._misc_info.update({key: value})
@@ -612,6 +623,7 @@ class BaseClass(Base):
         if dlg.exec():
             pass
 
+
 class LogMixin(Base):
     tracking_exclusion: ClassVar = ['artic_technician', 'clientsubmissionsampleassociation',
                                     'submission_reagent_associations', 'submission_equipment_associations',

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

@@ -149,12 +149,14 @@ class ClientSubmission(BaseClass, LogMixin):
                 pass
         # query = query.order_by(cls.submitted_date.desc())
         # NOTE: Split query results into pages of size {page_size}
-        if page_size > 0:
+        if page_size > 0 and limit == 0:
-            query = query.limit(page_size)
+            limit = page_size
         page = page - 1
         if page is not None:
-            query = query.offset(page * page_size)
+            offset = page * page_size
-        return cls.execute_query(query=query, limit=limit, **kwargs)
+        else:
+            offset = None
+        return cls.execute_query(query=query, limit=limit, offset=offset, **kwargs)
 
     @classmethod
     def submissions_to_df(cls, submissiontype: str | None = None, limit: int = 0,
@@ -269,7 +271,9 @@ class ClientSubmission(BaseClass, LogMixin):
         try:
             assert isinstance(sample, Sample)
         except AssertionError:
+            logger.warning(f"Converting {sample} to sql.")
             sample = sample.to_sql()
+        logger.debug(sample.__dict__)
         try:
             row = sample._misc_info['row']
         except (KeyError, AttributeError):
@@ -278,10 +282,12 @@ class ClientSubmission(BaseClass, LogMixin):
             column = sample._misc_info['column']
         except KeyError:
             column = 0
+        logger.debug(f"Sample: {sample}")
+        submission_rank = sample._misc_info['submission_rank']
         assoc = ClientSubmissionSampleAssociation(
             sample=sample,
             submission=self,
-            submission_rank=sample._misc_info['submission_rank'],
+            submission_rank=submission_rank,
             row=row,
             column=column
         )
@@ -310,8 +316,9 @@ class ClientSubmission(BaseClass, LogMixin):
             for sample in active_samples:
                 sample = sample.to_sql()
                 logger.debug(f"Sample: {sample.id}")
-                assoc = run.add_sample(sample)
+                if sample not in run.sample:
-                assoc.save()
+                    assoc = run.add_sample(sample)
+                    assoc.save()
         else:
             logger.warning("Run cancelled.")
         obj.set_data()

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

@@ -43,9 +43,10 @@ class DefaultParser(object):
         """
         self.proceduretype = proceduretype
         try:
-            self._pyd_object = getattr(pydant, f"Pyd{self.__class__.__name__.replace('Parser', '')}")
+            self._pyd_object = getattr(pydant, f"Pyd{self.__class__.__name__.replace('Parser', '').replace('Info', '')}")
-        except AttributeError:
+        except AttributeError as e:
-            self._pyd_object = pydant.PydResults
+            logger.error(f"Couldn't get pyd object: Pyd{self.__class__.__name__.replace('Parser', '').replace('Info', '')}")
+            self._pyd_object = getattr(pydant, self.__class__.pyd_name)
         self.workbook = load_workbook(self.filepath, data_only=True)
         if not range_dict:
             self.range_dict = self.__class__.default_range_dict
@@ -118,7 +119,7 @@ class DefaultTABLEParser(DefaultParser):
                     if isinstance(key, str):
                         key = key.lower().replace(" ", "_")
                         key = re.sub(r"_(\(.*\)|#)", "", key)
-                    logger.debug(f"Row {ii} values: {key}: {value}")
+                    # logger.debug(f"Row {ii} values: {key}: {value}")
                     output[key] = value
                 yield output
 
@@ -126,4 +127,4 @@ class DefaultTABLEParser(DefaultParser):
         return [self._pyd_object(**output) for output in self.parsed_info]
 
 from .clientsubmission_parser import *
-from backend.excel.parsers.results_parsers.pcr_results_parser import *
+from backend.excel.parsers.results_parsers.pcr_results_parser import PCRInfoParser, PCRSampleParser

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

@@ -74,6 +74,8 @@ class ClientSubmissionInfoParser(DefaultKEYVALUEParser, SubmissionTyperMixin):
     Object for retrieving submitter info from "sample list" sheet
     """
 
+    pyd_name = "PydClientSubmission"
+
     default_range_dict = [dict(
         start_row=2,
         end_row=18,
@@ -110,6 +112,8 @@ class ClientSubmissionSampleParser(DefaultTABLEParser, SubmissionTyperMixin):
     Object for retrieving submitter samples from "sample list" sheet
     """
 
+    pyd_name = "PydSample"
+
     default_range_dict = [dict(
         header_row=19,
         end_row=115,
@@ -126,7 +130,7 @@ class ClientSubmissionSampleParser(DefaultTABLEParser, SubmissionTyperMixin):
     def parsed_info(self) -> Generator[dict, None, None]:
         output = super().parsed_info
         for ii, sample in enumerate(output):
-            logger.debug(f"Parsed info sample: {sample}")
+            # logger.debug(f"Parsed info sample: {sample}")
             if isinstance(sample["row"], str) and sample["row"].lower() in ascii_lowercase[0:8]:
                 try:
                     sample["row"] = row_keys[sample["row"]]

src/submissions/backend/validators/pydant.py

@@ -290,6 +290,16 @@ class PydSample(PydBaseClass):
             value = row_keys[value]
         return value
 
+    def improved_dict(self, dictionaries: bool = True) -> dict:
+        output = super().improved_dict(dictionaries=dictionaries)
+        output['name'] = self.sample_id
+        del output['sampletype']
+        return output
+
+    def to_sql(self):
+        sql = super().to_sql()
+        sql._misc_info["submission_rank"] = self.submission_rank
+        return sql
 
 class PydTips(BaseModel):
     name: str

src/submissions/frontend/widgets/procedure_creation.py

@@ -90,7 +90,7 @@ class ProcedureCreation(QDialog):
             plate_map=self.plate_map,
             edit=self.edit
         )
-        with open("web.html", "w") as f:
+        with open("procedure_creation_rendered.html", "w") as f:
             f.write(html)
         self.webview.setHtml(html)
 

src/submissions/frontend/widgets/sample_checker.py

@@ -5,11 +5,9 @@ from PyQt6.QtCore import Qt, pyqtSlot
 from PyQt6.QtWebChannel import QWebChannel
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtWidgets import QDialog, QDialogButtonBox, QGridLayout
-
 from backend.db.models import ClientSubmission
 from backend.validators import PydSample, RSLNamer
-from tools import get_application_from_parent, jinja_template_loading
+from tools import get_application_from_parent, jinja_template_loading, render_details_template
-
 
 env = jinja_template_loading()
 
@@ -24,6 +22,7 @@ class SampleChecker(QDialog):
             self.rsl_plate_number = RSLNamer.construct_new_plate_name(clientsubmission.to_dict())
         else:
             self.rsl_plate_number = clientsubmission
+        logger.debug(f"RSL Plate number: {self.rsl_plate_number}")
         self.samples = samples
         self.setWindowTitle(title)
         self.app = get_application_from_parent(parent)
@@ -38,22 +37,27 @@ class SampleChecker(QDialog):
         # NOTE: Used to maintain javascript functions.
         template = env.get_template("sample_checker.html")
         template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
-        with open(template_path.joinpath("css", "styles.css"), "r") as f:
+        # with open(template_path.joinpath("css", "styles.css"), "r") as f:
-            css = f.read()
+        #     css = [f.read()]
         try:
             samples = self.formatted_list
         except AttributeError as e:
             logger.error(f"Problem getting sample list: {e}")
             samples = []
-        html = template.render(samples=samples, css=css, rsl_plate_number=self.rsl_plate_number)
+        # html = template.render(samples=samples, css=css, rsl_plate_number=self.rsl_plate_number)
+        html = render_details_template(template_name="sample_checker", samples=samples, rsl_plate_number=self.rsl_plate_number)
         self.webview.setHtml(html)
+        self.webview.page().setWebChannel(self.channel)
         QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
         self.buttonBox = QDialogButtonBox(QBtn)
         self.buttonBox.accepted.connect(self.accept)
         self.buttonBox.rejected.connect(self.reject)
         self.layout.addWidget(self.buttonBox, 11, 9, 1, 1, alignment=Qt.AlignmentFlag.AlignRight)
         self.setLayout(self.layout)
-        self.webview.page().setWebChannel(self.channel)
+
+        with open("sample_checker_rendered.html", "w") as f:
+            f.write(html)
+        logger.debug(f"HTML sample checker written!")
 
     @pyqtSlot(str, str, str)
     def text_changed(self, submission_rank: str, key: str, new_value: str):
@@ -65,8 +69,8 @@ class SampleChecker(QDialog):
             return
         item.__setattr__(key, new_value)
 
-    @pyqtSlot(str, bool)
+    @pyqtSlot(int, bool)
-    def enable_sample(self, submission_rank: str, enabled: bool):
+    def enable_sample(self, submission_rank: int, enabled: bool):
         logger.debug(f"Name: {submission_rank}, Enabled: {enabled}")
         try:
             item = next((sample for sample in self.samples if int(submission_rank) == sample.submission_rank))

src/submissions/frontend/widgets/submission_table.py

@@ -325,8 +325,9 @@ class SubmissionsTree(QTreeView):
         """
         indexes = self.selectedIndexes()
         dicto = next((item.data(1) for item in indexes if item.data(1)))
+        logger.debug(f"Dicto: {pformat(dicto)}")
         query_obj = dicto['item_type'].query(name=dicto['query_str'], limit=1)
-        logger.debug(query_obj)
+        logger.debug(f"Querying: {query_obj}")
         # NOTE: Convert to data in id column (i.e. column 0)
         # id = id.sibling(id.row(), 0).data()
         # logger.debug(id.model().query_group_object(id.row()))

src/submissions/frontend/widgets/submission_widget.py

@@ -141,6 +141,11 @@ class SubmissionFormContainer(QWidget):
         checker = SampleChecker(self, "Sample Checker", self.pydsamples)
         if checker.exec():
             # logger.debug(pformat(self.pydclientsubmission.sample))
+            try:
+                assert isinstance(self.pydclientsubmission, PydClientSubmission)
+            except AssertionError as e:
+                logger.error(f"Got wrong type for {self.pydclientsubmission}: {type(self.pydclientsubmission)}")
+                raise e
             self.form = self.pydclientsubmission.to_form(parent=self)
             self.form.samples = self.pydsamples
             self.layout().addWidget(self.form)

src/submissions/templates/details.html

@@ -24,23 +24,23 @@
 
 {% block script %}
 {% if not child %}
-<script>
+<!--<script>-->
-var coll = document.getElementsByClassName("collapsible");
+<!--var coll = document.getElementsByClassName("collapsible");-->
-var i;
+<!--var i;-->
 
-for (i = 0; i < coll.length; i++) {
+<!--for (i = 0; i < coll.length; i++) {-->
-  coll[i].addEventListener("click", function() {
+<!--  coll[i].addEventListener("click", function() {-->
-    this.classList.toggle("active");
+<!--    this.classList.toggle("active");-->
-    var content = this.nextElementSibling;
+<!--    var content = this.nextElementSibling;-->
-    if (content.style.display === "block") {
+<!--    if (content.style.display === "block") {-->
-      content.style.display = "none";
+<!--      content.style.display = "none";-->
-    } else {
+<!--    } else {-->
-      content.style.display = "block";
+<!--      content.style.display = "block";-->
-    }
+<!--    }-->
-  });
+<!--  });-->
-}
+<!--}-->
-</script>
+<!--</script>-->
-{% endif %}
+<!--{% endif %}-->
 {% for j in js%}
 
 <script>

src/submissions/templates/sample_checker.html

@@ -1,54 +1,60 @@
 {% extends "details.html" %}
-<head>
+<html>
-    {% block head %}
+    <head>
-    {{ super() }}
+        {% block head %}
-    <title>Sample Checker</title>
+        {{ super() }}
-    {% endblock %}
+        <title>Sample Checker</title>
-</head>
+        {% endblock %}
-<body>
+    </head>
-    {% block body %}
+    <body>
-    <h2><u>Sample Checker</u></h2>
+        {% block body %}
-    <br>
+        <h2><u>Sample Checker</u></h2>
-    {% if rsl_plate_num %}
+        <br>
-    <label for="rsl_plate_number">RSL Plate Number:</label><br>
+        {% if rsl_plate_number %}
-    <input type="text" id="rsl_plate_number" name="sample_id" value="{{ rsl_plate_number }}" size="40">
+        <label for="rsl_plate_number">RSL Plate Number:</label><br>
+        <input type="text" id="rsl_plate_number" name="sample_id" value="{{ rsl_plate_number }}" size="40">
+        {% endif %}
+        <br>
+        <p>Take a moment to verify sample names.</p>
+        <br>
+        <form>
+            &emsp;&emsp;Submitter ID<br/><!--&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;Row&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp; Column<br/>-->
+            {% for sample in samples %}
+                {% if rsl_plate_number %}<input type="checkbox" id="{{ sample['submission_rank'] }}_enabled" name="vehicle1" value="Bike" {% if sample['enabled'] %}checked{% endif %}>{% endif %}
+                {{ '%02d' % sample['submission_rank'] }}
+                <input type="text" id="{{ sample['submission_rank'] }}_id" name="sample_id" value="{{ sample['sample_id'] }}" size="40" style="color:{{ sample['color'] }};" {% if rsl_plate_number %}disabled{% endif %}>
+                <br/>
+            {% endfor %}
+        </form>
+        {% endblock %}
+    </body>
 
-    {% endif %}
+      {% block script %}
-    <br>
-    <p>Take a moment to verify sample names.</p>
-    <br>
-    <form>
-        &emsp;&emsp;Submitter ID<br/><!--&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;Row&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp;&emsp; Column<br/>-->
-        {% for sample in samples %}
-            {% if rsl_plate_num %}<input type="checkbox" id="{{ sample['submission_rank'] }}_enabled" name="vehicle1" value="Bike" {% if sample['enabled'] %}checked{% endif %}>{% endif %}
-            {{ '%02d' % sample['submission_rank'] }}
-            <input type="text" id="{{ sample['submission_rank'] }}_id" name="sample_id" value="{{ sample['sample_id'] }}" size="40" style="color:{{ sample['color'] }};" {% if rsl_plate_num %}disabled{% endif %}>
-<!--            <input type="number" id="{{ sample['submission_rank'] }}_row" name="row" value="{{ sample['row'] }}" size="5", min="1">-->
-<!--            <input type="number" id="{{ sample['submission_rank'] }}_col" name="column" value="{{ sample['column'] }}" size="5", min="1">-->
-            <br/>
-        {% endfor %}
-    </form>
-    {% endblock %}
-</body>
 
-  {% block script %}
+      <script>
-  {{ super() }}
+      {% for sample in samples %}
-  <script>
+      document.getElementById("{{ sample['submission_rank'] }}_id").addEventListener("input", function(){
-  {% for sample in samples %}
+          backend.text_changed("{{ sample['submission_rank'] }}", this.name, this.value);
-  document.getElementById("{{ sample['submission_rank'] }}_id").addEventListener("input", function(){
+      });
-      backend.text_changed("{{ sample['submission_rank'] }}", this.name, this.value);
+      {% if rsl_plate_number %}
-  });
+      document.getElementById("{{ sample['submission_rank'] }}_enabled").addEventListener("change", function(){
-  {% if rsl_plate_num %}
+          console.log(typeof({{ sample['submission_rank'] }}) + " " + typeof(this.checked));
-  document.getElementById("{{ sample['submission_rank'] }}_enabled").addEventListener("input", function(){
+          backend.enable_sample({{ sample['submission_rank'] }}, this.checked);
-      backend.enable_sample("{{ sample['submission_rank'] }}", this.checked);
+      });
-  });
+      {% endif %}
-  {% endif %}
+      {% endfor %}
-  {% endfor %}
+      </script>
-  document.addEventListener('DOMContentLoaded', function() {
+      <script>
-          backend.activate_export(false);
+      document.getElementById("rsl_plate_number").addEventListener("input", function(){
-      }, false);
+          console.log(this.value);
-  document.getElementById("rsl_plate_num").addEventListener("input", function(){
+          console.log(typeof(this.value));
-      backend.set_rsl_plate_num(this.value);
+          backend.set_rsl_plate_number(this.value);
-  });
+      });
-  </script>
+      </script>
-  {% endblock %}
+      <script>
+      document.addEventListener('DOMContentLoaded', function() {
+            backend.activate_export(false);
+        }, false);
+      </script>
+      {{ super() }}
+      {% endblock %}