Database updates, scraping samples from excel sheets

alembic/versions/03da9270e51f_initial_commit.py

@@ -1,8 +1,8 @@
 """initial commit
 
-Revision ID: 4cba0c1ffe03
+Revision ID: 03da9270e51f
 Revises: 
-Create Date: 2023-01-18 08:59:34.382715
+Create Date: 2023-01-19 09:01:03.022482
 
 """
 from alembic import op
@@ -10,7 +10,7 @@ import sqlalchemy as sa
 
 
 # revision identifiers, used by Alembic.
-revision = '4cba0c1ffe03'
+revision = '03da9270e51f'
 down_revision = None
 branch_labels = None
 depends_on = None
@@ -50,22 +50,6 @@ def upgrade() -> None:
     sa.ForeignKeyConstraint(['kit_id'], ['_kits.id'], name='fk_RT_kits_id', ondelete='SET NULL', use_alter=True),
     sa.PrimaryKeyConstraint('id')
     )
-    op.create_table('_ww_samples',
-    sa.Column('id', sa.INTEGER(), nullable=False),
-    sa.Column('ww_processing_num', sa.String(length=64), nullable=True),
-    sa.Column('ww_sample_full_id', sa.String(length=64), nullable=True),
-    sa.Column('rsl_number', sa.String(length=64), nullable=True),
-    sa.Column('collection_date', sa.TIMESTAMP(), nullable=True),
-    sa.Column('testing_type', sa.String(length=64), nullable=True),
-    sa.Column('site_status', sa.String(length=64), nullable=True),
-    sa.Column('notes', sa.String(length=2000), nullable=True),
-    sa.Column('ct_n1', sa.FLOAT(precision=2), nullable=True),
-    sa.Column('ct_n2', sa.FLOAT(precision=2), nullable=True),
-    sa.Column('seq_submitted', sa.BOOLEAN(), nullable=True),
-    sa.Column('ww_seq_run_id', sa.String(length=64), nullable=True),
-    sa.Column('sample_type', sa.String(length=8), nullable=True),
-    sa.PrimaryKeyConstraint('id')
-    )
     op.create_table('_control_samples',
     sa.Column('id', sa.INTEGER(), nullable=False),
     sa.Column('parent_id', sa.String(), nullable=True),
@@ -119,35 +103,63 @@ def upgrade() -> None:
     sa.Column('technician', sa.String(length=64), nullable=True),
     sa.Column('reagents_id', sa.String(), nullable=True),
     sa.Column('control_id', sa.INTEGER(), nullable=True),
-    sa.Column('sample_id', sa.String(), nullable=True),
     sa.ForeignKeyConstraint(['control_id'], ['_control_samples.id'], name='fk_BC_control_id', ondelete='SET NULL'),
-    sa.ForeignKeyConstraint(['extraction_kit_id'], ['_kits.id'], ondelete='SET NULL'),
+    sa.ForeignKeyConstraint(['extraction_kit_id'], ['_kits.id'], name='fk_BS_extkit_id', ondelete='SET NULL'),
     sa.ForeignKeyConstraint(['reagents_id'], ['_reagents.id'], name='fk_BS_reagents_id', ondelete='SET NULL'),
-    sa.ForeignKeyConstraint(['sample_id'], ['_ww_samples.id'], name='fk_WW_sample_id', ondelete='SET NULL'),
+    sa.ForeignKeyConstraint(['submitting_lab_id'], ['_organizations.id'], name='fk_BS_sublab_id', ondelete='SET NULL'),
-    sa.ForeignKeyConstraint(['submitting_lab_id'], ['_organizations.id'], ondelete='SET NULL'),
     sa.PrimaryKeyConstraint('id'),
     sa.UniqueConstraint('rsl_plate_num'),
     sa.UniqueConstraint('submitter_plate_num')
     )
+    op.create_table('_bc_samples',
+    sa.Column('id', sa.INTEGER(), nullable=False),
+    sa.Column('well_number', sa.String(length=8), nullable=True),
+    sa.Column('sample_id', sa.String(length=64), nullable=False),
+    sa.Column('organism', sa.String(length=64), nullable=True),
+    sa.Column('concentration', sa.String(length=16), nullable=True),
+    sa.Column('rsl_plate_id', sa.INTEGER(), nullable=True),
+    sa.ForeignKeyConstraint(['rsl_plate_id'], ['_submissions.id'], name='fk_BCS_sample_id', ondelete='SET NULL'),
+    sa.PrimaryKeyConstraint('id')
+    )
     op.create_table('_reagents_submissions',
     sa.Column('reagent_id', sa.INTEGER(), nullable=True),
     sa.Column('submission_id', sa.INTEGER(), nullable=True),
     sa.ForeignKeyConstraint(['reagent_id'], ['_reagents.id'], ),
     sa.ForeignKeyConstraint(['submission_id'], ['_submissions.id'], )
     )
+    op.create_table('_ww_samples',
+    sa.Column('id', sa.INTEGER(), nullable=False),
+    sa.Column('ww_processing_num', sa.String(length=64), nullable=True),
+    sa.Column('ww_sample_full_id', sa.String(length=64), nullable=False),
+    sa.Column('rsl_number', sa.String(length=64), nullable=True),
+    sa.Column('rsl_plate_id', sa.INTEGER(), nullable=True),
+    sa.Column('collection_date', sa.TIMESTAMP(), nullable=True),
+    sa.Column('testing_type', sa.String(length=64), nullable=True),
+    sa.Column('site_status', sa.String(length=64), nullable=True),
+    sa.Column('notes', sa.String(length=2000), nullable=True),
+    sa.Column('ct_n1', sa.FLOAT(precision=2), nullable=True),
+    sa.Column('ct_n2', sa.FLOAT(precision=2), nullable=True),
+    sa.Column('seq_submitted', sa.BOOLEAN(), nullable=True),
+    sa.Column('ww_seq_run_id', sa.String(length=64), nullable=True),
+    sa.Column('sample_type', sa.String(length=8), nullable=True),
+    sa.Column('well_number', sa.String(length=8), nullable=True),
+    sa.ForeignKeyConstraint(['rsl_plate_id'], ['_submissions.id'], name='fk_WWS_sample_id', ondelete='SET NULL'),
+    sa.PrimaryKeyConstraint('id')
+    )
     # ### end Alembic commands ###
 
 
 def downgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('_ww_samples')
     op.drop_table('_reagents_submissions')
+    op.drop_table('_bc_samples')
     op.drop_table('_submissions')
     op.drop_table('_orgs_contacts')
     op.drop_table('_reagentstypes_kittypes')
     op.drop_table('_reagents')
     op.drop_table('_organizations')
     op.drop_table('_control_samples')
-    op.drop_table('_ww_samples')
     op.drop_table('_reagent_types')
     op.drop_table('_kits')
     op.drop_table('_control_types')

src/submissions/backend/db/__init__.py

@@ -16,6 +16,12 @@ def get_kits_by_use( ctx:dict, kittype_str:str|None) -> list:
 
 
 def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None:
+    for sample in base_submission.samples:
+        sample.rsl_plate = base_submission
+        try:
+            ctx['database_session'].add(sample)
+        except IntegrityError:
+            continue
     ctx['database_session'].add(base_submission)
     try:
         ctx['database_session'].commit()
@@ -53,6 +59,11 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
                 # Because of unique constraint, the submitter plate number cannot be None, so...
                 if info_dict[item] == None:
                     info_dict[item] = uuid.uuid4().hex.upper()
+                field_value = info_dict[item]
+            # case "samples":
+            #     for sample in info_dict[item]:
+            #         instance.samples.append(sample)
+            #     continue
             case _:
                 field_value = info_dict[item]
         try:
@@ -60,6 +71,7 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
         except AttributeError:
             print(f"Could not set attribute: {item} to {info_dict[item]}")
             continue
+    # print(instance.__dict__)
     return instance
     # looked_up = []
     # for reagent in reagents:
@@ -185,6 +197,10 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
         ctx (dict): Context dictionary passed down from frontend
         exp (dict): Experiment dictionary created from yaml file
     """
+    try:
+        exp['password'].decode()
+    except (UnicodeDecodeError, AttributeError):
+        exp['password'] = exp['password'].encode()
     if base64.b64encode(exp['password']) != b'cnNsX3N1Ym1pNTVpb25z':
         print(f"Not the correct password.")
         return

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

@@ -8,4 +8,4 @@ from .controls import Control, ControlType
 from .kits import KitType, ReagentType, Reagent
 from .submissions import BasicSubmission, BacterialCulture, Wastewater
 from .organizations import Organization, Contact
-from .samples import Sample
+from .samples import WWSample, BCSample

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

@@ -3,15 +3,16 @@ from sqlalchemy import Column, String, TIMESTAMP, text, JSON, INTEGER, ForeignKe
 from sqlalchemy.orm import relationship, relationships
 
 
-class Sample(Base):
+class WWSample(Base):
 
     __tablename__ = "_ww_samples"
 
     id = Column(INTEGER, primary_key=True) #: primary key
     ww_processing_num = Column(String(64))
-    ww_sample_full_id = Column(String(64))
+    ww_sample_full_id = Column(String(64), nullable=False)
     rsl_number = Column(String(64))
     rsl_plate = relationship("Wastewater", back_populates="samples")
+    rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_WWS_sample_id"))
     collection_date = Column(TIMESTAMP) #: Date submission received
     testing_type = Column(String(64))
     site_status = Column(String(64))
@@ -21,7 +22,35 @@ class Sample(Base):
     seq_submitted = Column(BOOLEAN())
     ww_seq_run_id = Column(String(64))
     sample_type = Column(String(8))
+    well_number = Column(String(8))
+
+    def to_string(self):
+        return f"{self.well_number}: {self.ww_sample_full_id}"
+
+    def to_sub_dict(self):
+        return {
+            "well": self.well_number,
+            "name": self.ww_sample_full_id,
+        }
 
 
+class BCSample(Base):
 
+    __tablename__ = "_bc_samples"
 
+    id = Column(INTEGER, primary_key=True) #: primary key
+    well_number = Column(String(8))
+    sample_id = Column(String(64), nullable=False)
+    organism = Column(String(64))
+    concentration = Column(String(16))
+    rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_BCS_sample_id"))
+    rsl_plate = relationship("BacterialCulture", back_populates="samples")
+
+    def to_string(self):
+        return f"{self.well_number}: {self.sample_id} - {self.organism}"
+
+    def to_sub_dict(self):
+        return {
+            "well": self.well_number,
+            "name": f"{self.sample_id} - ({self.organism})",
+        }

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

@@ -15,10 +15,10 @@ class BasicSubmission(Base):
     submitter_plate_num = Column(String(127), unique=True) #: The number given to the submission by the submitting lab
     submitted_date = Column(TIMESTAMP) #: Date submission received
     submitting_lab = relationship("Organization", back_populates="submissions") #: client
-    submitting_lab_id = Column(INTEGER, ForeignKey("_organizations.id", ondelete="SET NULL"))
+    submitting_lab_id = Column(INTEGER, ForeignKey("_organizations.id", ondelete="SET NULL", name="fk_BS_sublab_id"))
     sample_count = Column(INTEGER) #: Number of samples in the submission
     extraction_kit = relationship("KitType", back_populates="submissions") #: The extraction kit used
-    extraction_kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL"))
+    extraction_kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", name="fk_BS_extkit_id"))
     submission_type = Column(String(32))
     technician = Column(String(64))
     # Move this into custom types?
@@ -94,10 +94,12 @@ class BasicSubmission(Base):
 class  BacterialCulture(BasicSubmission):
     control = relationship("Control", back_populates="submissions") #: A control sample added to submission
     control_id = Column(INTEGER, ForeignKey("_control_samples.id", ondelete="SET NULL", name="fk_BC_control_id"))
+    samples = relationship("BCSample", back_populates="rsl_plate", uselist=True)
+    # bc_sample_id = Column(INTEGER, ForeignKey("_bc_samples.id", ondelete="SET NULL", name="fk_BC_sample_id"))
     __mapper_args__ = {"polymorphic_identity": "bacterial_culture", "polymorphic_load": "inline"}
     
 
 class Wastewater(BasicSubmission):
-    samples = relationship("Sample", back_populates="rsl_plate")
+    samples = relationship("WWSample", back_populates="rsl_plate", uselist=True)
-    sample_id = Column(String, ForeignKey("_ww_samples.id", ondelete="SET NULL", name="fk_WW_sample_id"))
+    # ww_sample_id = Column(String, ForeignKey("_ww_samples.id", ondelete="SET NULL", name="fk_WW_sample_id"))
     __mapper_args__ = {"polymorphic_identity": "wastewater", "polymorphic_load": "inline"}

src/submissions/backend/excel/parser.py

@@ -1,9 +1,12 @@
 import pandas as pd
 from pathlib import Path
-from datetime import datetime
+from backend.db.models.samples import WWSample, BCSample
 import logging
 from collections import OrderedDict
 import re
+import numpy as np
+from datetime import date
+import uuid
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -21,8 +24,8 @@ class SheetParser(object):
                 self.xl = None
         self.sub = OrderedDict()
         self.sub['submission_type'] = self._type_decider()        
-        parse = getattr(self, f"_parse_{self.sub['submission_type'].lower()}")
+        parse_sub = getattr(self, f"_parse_{self.sub['submission_type'].lower()}")
-        parse()
+        parse_sub()
 
     def _type_decider(self):
         try:
@@ -46,6 +49,7 @@ class SheetParser(object):
         self.sub['submitting_lab'] = submission_info.iloc[0][3]
         self.sub['sample_count'] = str(submission_info.iloc[2][3])
         self.sub['extraction_kit'] = submission_info.iloc[3][3]
+        
         return submission_info
 
 
@@ -71,6 +75,9 @@ class SheetParser(object):
         self.sub['lot_ethanol'] = submission_info.iloc[10][6]
         self.sub['lot_positive_control'] = submission_info.iloc[103][1]
         self.sub['lot_plate'] = submission_info.iloc[12][6]
+        sample_parser = SampleParser(submission_info.iloc[15:111])
+        sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
+        self.sub['samples'] = sample_parse()
 
 
     def _parse_wastewater(self):
@@ -102,6 +109,9 @@ class SheetParser(object):
         self.sub['lot_pre_mix_2'] = qprc_info.iloc[2][14]
         self.sub['lot_positive_control'] = qprc_info.iloc[3][14]
         self.sub['lot_ddh2o'] = qprc_info.iloc[4][14]
+        sample_parser = SampleParser(submission_info.iloc[16:40])
+        sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
+        self.sub['samples'] = sample_parse()
         # tech = str(submission_info.iloc[11][1])
         # if tech == "nan":
         #     tech = "Unknown"
@@ -120,3 +130,59 @@ class SheetParser(object):
         # self.sub['lot_ethanol'] = submission_info.iloc[10][6]
         # self.sub['lot_positive_control'] = None #submission_info.iloc[103][1]
         # self.sub['lot_plate'] = submission_info.iloc[12][6]
+
+
+class SampleParser(object):
+
+
+    def __init__(self, df:pd.DataFrame) -> None:
+        self.samples = df.to_dict("records")
+
+
+    def parse_bacterial_culture_samples(self) -> list[BCSample]:
+        new_list = []
+        for sample in self.samples:
+            new = BCSample()
+            new.well_number = sample['This section to be filled in completely by submittor']
+            new.sample_id = sample['Unnamed: 1']
+            new.organism = sample['Unnamed: 2']
+            new.concentration = sample['Unnamed: 3']
+            print(f"Sample object: {new.sample_id} = {type(new.sample_id)}")
+            try:
+                not_a_nan = not np.isnan(new.sample_id)
+            except TypeError:
+                not_a_nan = True
+            if not_a_nan:
+                new_list.append(new)
+        return new_list
+
+
+    def parse_wastewater_samples(self) -> list[WWSample]:
+        new_list = []
+        for sample in self.samples:
+            new = WWSample()
+            new.ww_processing_num = sample['Unnamed: 2']
+            try:
+                not_a_nan = not np.isnan(sample['Unnamed: 3'])
+            except TypeError:
+                not_a_nan = True
+            if not_a_nan:
+                new.ww_sample_full_id = sample['Unnamed: 3']
+            else:
+                new.ww_sample_full_id = uuid.uuid4().hex.upper()
+            new.rsl_number = sample['Unnamed: 9']
+            try:
+                not_a_nan = not np.isnan(sample['Unnamed: 5'])
+            except TypeError:
+                not_a_nan = True
+            if not_a_nan:
+                new.collection_date = sample['Unnamed: 5']
+            else:
+                new.collection_date = date.today()
+            new.testing_type = sample['Unnamed: 6']
+            new.site_status = sample['Unnamed: 7']
+            new.notes = str(sample['Unnamed: 8'])
+            new.well_number = sample['Unnamed: 1']
+            new_list.append(new)
+        return new_list
+    

src/submissions/frontend/__init__.py

@@ -90,6 +90,7 @@ class App(QMainWindow):
 
     def importSubmission(self):
         logger.debug(self.ctx)
+        self.samples = []
         home_dir = str(Path(self.ctx["directory_path"]))
         fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir)[0])
         logger.debug(f"Attempting to parse file: {fname}")
@@ -107,27 +108,31 @@ class App(QMainWindow):
             (?P<extraction_kit>^extraction_kit$) |
             (?P<submitted_date>^submitted_date$) |
             (?P<submitting_lab>)^submitting_lab$ |
+            (?P<samples>)^samples$ |
             (?P<reagent>^lot_.*$)
 
         """, re.VERBOSE)
         for item in prsr.sub:
             logger.debug(f"Item: {item}")
-            self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
+            
             try:
                 mo = variable_parser.fullmatch(item).lastgroup
             except AttributeError:
                 mo = "other"
+            print(f"Mo: {mo}")
             match mo:
                 case 'submitting_lab':
+                    self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
                     print(f"{item}: {prsr.sub[item]}")
                     add_widget = QComboBox()
                     labs = [item.__str__() for item in lookup_all_orgs(ctx=self.ctx)]
                     try:
                         labs = difflib.get_close_matches(prsr.sub[item], labs, len(labs), 0)
-                    except TypeError:
+                    except (TypeError, ValueError):
                         pass
                     add_widget.addItems(labs)
                 case 'extraction_kit':
+                    self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
                     if prsr.sub[item] == 'nan':
                         msg = QMessageBox()
                         # msg.setIcon(QMessageBox.critical)
@@ -143,10 +148,12 @@ class App(QMainWindow):
                     else:
                         add_widget.addItems(['bacterial_culture'])
                 case 'submitted_date':
+                    self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
                     add_widget = QDateEdit(calendarPopup=True)
                     # add_widget.setDateTime(QDateTime.date(prsr.sub[item]))
                     add_widget.setDate(prsr.sub[item])
                 case 'reagent':
+                    self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
                     add_widget = QComboBox()
                     add_widget.setEditable(True)
                     # Ensure that all reagenttypes have a name that matches the items in the excel parser
@@ -169,7 +176,12 @@ class App(QMainWindow):
                             relevant_reagents.insert(0, str(prsr.sub[item]))
                     logger.debug(f"Relevant reagents: {relevant_reagents}")
                     add_widget.addItems(relevant_reagents)
+                # TODO: make samples not appear in frame.
+                case 'samples':
+                    print(f"{item}: {prsr.sub[item]}")
+                    self.samples = prsr.sub[item]
                 case _:
+                    self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
                     add_widget = QLineEdit()
                     add_widget.setText(str(prsr.sub[item]).replace("_", " "))
             self.table_widget.formlayout.addWidget(add_widget)
@@ -215,6 +227,7 @@ class App(QMainWindow):
             if wanted_reagent != None:
                 parsed_reagents.append(wanted_reagent)
                 logger.debug(info)
+        info['samples'] = self.samples
         base_submission = construct_submission_info(ctx=self.ctx, info_dict=info)
         for reagent in parsed_reagents:
             base_submission.reagents.append(reagent)

src/submissions/frontend/custom_widgets/__init__.py

@@ -4,7 +4,7 @@ from PyQt6.QtWidgets import (
     QDialogButtonBox, QDateEdit, QTableView,
     QTextEdit, QSizePolicy, QWidget,
     QGridLayout, QPushButton, QSpinBox,
-    QScrollBar
+    QScrollBar, QScrollArea
 )
 from PyQt6.QtCore import Qt, QDate, QAbstractTableModel
 from PyQt6.QtGui import QFontMetrics
@@ -135,6 +135,7 @@ class SubmissionsSheet(QTableView):
         # print(index)
         value=index.sibling(index.row(),0).data()
         dlg = SubmissionDetails(ctx=self.ctx, id=value)
+        # dlg.show()
         if dlg.exec():
             pass
 
@@ -146,32 +147,42 @@ class SubmissionDetails(QDialog):
         super().__init__()
 
         self.setWindowTitle("Submission Details")
+        interior = QScrollArea()
+        interior.setParent(self)
         data = lookup_submission_by_id(ctx=ctx, id=id)
         base_dict = data.to_dict()
         base_dict['reagents'] = [item.to_sub_dict() for item in data.reagents]
+        base_dict['samples'] = [item.to_sub_dict() for item in data.samples]
         template = env.get_template("submission_details.txt")
         text = template.render(sub=base_dict)
-        txt_field = QTextEdit(self)
+        txt_editor = QTextEdit(self)
-        txt_field.setReadOnly(True)
-        txt_field.document().setPlainText(text)
         
-        font = txt_field.document().defaultFont()
+        txt_editor.setReadOnly(True)
+        txt_editor.document().setPlainText(text)
+        
+        font = txt_editor.document().defaultFont()
         fontMetrics = QFontMetrics(font)
-        textSize = fontMetrics.size(0, txt_field.toPlainText())
+        textSize = fontMetrics.size(0, txt_editor.toPlainText())
 
         w = textSize.width() + 10
         h = textSize.height() + 10
-        txt_field.setMinimumSize(w, h)
+        txt_editor.setMinimumSize(w, h)
-        txt_field.setMaximumSize(w, h)
+        txt_editor.setMaximumSize(w, h)
-        txt_field.resize(w, h)
+        txt_editor.resize(w, h)
+        interior.resize(w,900)
         # txt_field.setSizePolicy(QSizePolicy.Policy.Preferred, QSizePolicy.Policy.MinimumExpanding)
-        QBtn = QDialogButtonBox.StandardButton.Ok
+        # QBtn = QDialogButtonBox.StandardButton.Ok
         # self.buttonBox = QDialogButtonBox(QBtn)
         # self.buttonBox.accepted.connect(self.accept)
-        txt_field.setText(text)
+        txt_editor.setText(text)
+        # txt_editor.verticalScrollBar()
+        interior.setWidget(txt_editor)
         self.layout = QVBoxLayout()
-        self.layout.addWidget(txt_field)
+        self.setFixedSize(w, 900)
+        # self.layout.addWidget(txt_editor)
         # self.layout.addStretch()
+        self.layout.addWidget(interior)
+        
 
 
 class ReportDatePicker(QDialog):

src/submissions/templates/submission_details.txt

@@ -1,9 +1,13 @@
 
 
-{% for key, value in sub.items() if key != 'reagents' %}
+{% for key, value in sub.items() if key != 'reagents' and key != 'samples' %}
 {{ key }}: {{ value }}
 {% endfor %}
 Reagents:
 {% for item in sub['reagents'] %}
     {{ item['type'] }}: {{ item['lot'] }} (EXP: {{ item['expiry'] }})
 {% endfor %}
+Samples:
+{% for item in sub['samples'] %}
+    {{ item['well'] }}: {{ item['name'] }}
+{% endfor %}