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Add in missing product link
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@daveih
daveih committed Feb 4, 2025
1 parent 17c0f1b commit 000e8df
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Showing 4 changed files with 31 additions and 15 deletions.
8 changes: 6 additions & 2 deletions src/usdm_excel/study_design_intervention_sheet/study_design_intervention_sheet.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
from usdm_model.study_intervention import StudyIntervention
from usdm_model.administration import Administration
from usdm_model.administration_duration import AdministrationDuration
from usdm_model.administrable_product import AdministrableProduct
from usdm_excel.globals import Globals

class StudyDesignInterventionSheet(BaseSheet):
Expand Down Expand Up @@ -33,7 +34,6 @@ def _create_intervention(self, index, agent_admin):
'codes': self.read_other_code_cell_multiple_by_name(index, "codes"),
'role': self.read_cdisc_klass_attribute_cell_by_name("StudyIntervention", "role", index, "role"),
'type': self.read_cdisc_klass_attribute_cell_by_name("StudyIntervention", "type", index, "type"),
#'productDesignation': self.read_cdisc_klass_attribute_cell_by_name("StudyIntervention", "productDesignation", index, "productDesignation"),
'minimumResponseDuration': self.read_quantity_cell_by_name(index, "minimumResponseDuration"),
'administrations': [agent_admin]
}
Expand All @@ -46,14 +46,18 @@ def _create_intervention(self, index, agent_admin):
self.current_intervention.administrations.append(agent_admin)

def _create_administration(self, index, admin_duration):
product_name = self.read_cell_by_name(index, "product", must_be_present=False)
product = self.globals.cross_references.get(AdministrableProduct, product_name)
product_id = product.id if product else None
params = {
'name': self.read_cell_by_name(index, 'administrationName'),
'description': self.read_cell_by_name(index, 'administrationDescription', must_be_present=False),
'label': self.read_cell_by_name(index, 'administrationLabel', must_be_present=False),
'duration': admin_duration,
'dose': self.read_quantity_cell_by_name(index, "administrationDose"),
'route': Alias(self.globals).code(self.read_cdisc_klass_attribute_cell_by_name("Administration", "route", index, "administrationRoute"), []),
'frequency': Alias(self.globals).code(self.read_cdisc_klass_attribute_cell_by_name("Administration", "frequency", index, "administrationFrequency"), [])
'frequency': Alias(self.globals).code(self.read_cdisc_klass_attribute_cell_by_name("Administration", "frequency", index, "administrationFrequency"), []),
'administrableProductId': product_id,
}
item = self.create_object(Administration, params)
if item:
Expand Down
4 changes: 2 additions & 2 deletions tests/integration_test_files/devices.json
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Original file line number Diff line number Diff line change
Expand Up @@ -8994,7 +8994,7 @@
"standardCodeAliases": [],
"instanceType": "AliasCode"
},
"administrableProductId": null,
"administrableProductId": "AdministrableProduct_1",
"medicalDeviceId": null,
"notes": [],
"instanceType": "Administration"
Expand Down Expand Up @@ -9127,7 +9127,7 @@
"standardCodeAliases": [],
"instanceType": "AliasCode"
},
"administrableProductId": null,
"administrableProductId": "AdministrableProduct_1",
"medicalDeviceId": null,
"notes": [],
"instanceType": "Administration"
Expand Down
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34 changes: 23 additions & 11 deletions tests/test_study_design_intervention_sheet.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,13 +3,15 @@
import pandas as pd
from usdm_excel.study_design_intervention_sheet.study_design_intervention_sheet import StudyDesignInterventionSheet
from usdm_model.code import Code

from usdm_model.administrable_product import AdministrableProduct
from usdm_excel.globals import Globals
from tests.test_factory import Factory

xfail = pytest.mark.xfail

SAVE = True
COLUMNS = [ 'name', 'description', 'label', "codes", "role", "type",
"pharmacologicalClass", "productDesignation", "minimumResponseDuration", 'administrationName', 'administrationDescription',
"product", "minimumResponseDuration", 'administrationName', 'administrationDescription',
'administrationLabel', "administrationRoute", "administrationDose", "administrationFrequency",
'administrationDurationDescription', 'administrationDurationWillVary', 'administrationDurationWillVaryReason', 'administrationDurationQuantity' ]

Expand All @@ -21,8 +23,10 @@ def read_json(filename):
def dump_json(data):
print(f"\n{json.dumps(data, indent=2)}")

def test_create(mocker, globals):
def test_create(mocker, globals: Globals, factory: Factory):
mock_id = mocker.patch("usdm_excel.id_manager.IdManager.build_id")
mock_id.side_effect=[f"pid_{x}" for x in range(10)]
_create_products(factory, globals)
mock_id.side_effect=[f"Id_{x}" for x in range(100)]

mock_code = mocker.patch("usdm_excel.cdisc_ct.CDISCCT.code_for_attribute")
Expand All @@ -32,12 +36,12 @@ def test_create(mocker, globals):
mocker.patch("builtins.open", mocked_open)
# productDesignation now removed but leave in data, wont do any harm as it is ignored. Also see COLUMNS above.
data = [
# name description label codes role type pharmacologicalClass productDesignation minimumResponseDuration, administrationName [10] administrationDescription administrationLabel administrationRoute administrationDose administrationFrequency administrationDurationDescription administrationDurationWillVary administrationDurationWillVaryReason administrationDurationQuantity
[ 'Int 1', 'Int Desc 1', 'Int Label 1', 'SPONSOR: A=B', 'Experimental Intervention', 'C12345', 'FDA: A=B', 'IMP', '1 Day', 'Admin 1', 'Admin Desc 1', 'Admin Label 1', 'C345671', '12 mg', 'C65432', 'Dur desc 1', 'False', '', '14 %' ],
[ '', '', '', '', '', '', '', '', '', 'Admin 2', 'Admin Desc 2', 'Admin Label 1', 'C345672', '1 mg', 'C65432', 'Dur desc 1', 'False', '', '10 m' ],
[ 'Int 2', 'Int Desc 2', 'Int Label 2', 'SPONSOR: C=D', 'Placebo', 'C12346', 'FDA: A=B', 'NIMP (AxMP)', '3 Weeks', 'Admin 3', 'Admin Desc 3', 'Admin Label 1', 'C345673', '100 mg', 'C65432', 'Dur desc 1', 'False', '', '12 C' ],
[ 'Int 3', 'Int Desc 3', 'Int Label 3', 'SPONSOR: E=F, SPONSOR: G=H', 'Rescue Medicine', 'C12347', 'FDA: A=B', 'IMP', '4 Years', 'Admin 4', 'Admin Desc 4', 'Admin Label 1', 'C345674', '500 mg', 'C65432', 'Dur desc 1', 'False', '', '12 F' ],
[ '', '', '', '', '', '', '', '', '', 'Admin 5', 'Admin Desc 5', 'Admin Label 1', 'C345675', '1 mg', 'C65432', 'Dur desc 1', 'False', '', '15 in' ],
# name description label codes role type product minimumResponseDuration, administrationName [10] administrationDescription administrationLabel administrationRoute administrationDose administrationFrequency administrationDurationDescription administrationDurationWillVary administrationDurationWillVaryReason administrationDurationQuantity
[ 'Int 1', 'Int Desc 1', 'Int Label 1', 'SPONSOR: A=B', 'Experimental Intervention', 'C12345', 'Product 1', '1 Day', 'Admin 1', 'Admin Desc 1', 'Admin Label 1', 'C345671', '12 mg', 'C65432', 'Dur desc 1', 'False', '', '14 %' ],
[ '', '', '', '', '', '', '', '', 'Admin 2', 'Admin Desc 2', 'Admin Label 1', 'C345672', '1 mg', 'C65432', 'Dur desc 1', 'False', '', '10 m' ],
[ 'Int 2', 'Int Desc 2', 'Int Label 2', 'SPONSOR: C=D', 'Placebo', 'C12346', '', '3 Weeks', 'Admin 3', 'Admin Desc 3', 'Admin Label 1', 'C345673', '100 mg', 'C65432', 'Dur desc 1', 'False', '', '12 C' ],
[ 'Int 3', 'Int Desc 3', 'Int Label 3', 'SPONSOR: E=F, SPONSOR: G=H', 'Rescue Medicine', 'C12347', '', '4 Years', 'Admin 4', 'Admin Desc 4', 'Admin Label 1', 'C345674', '500 mg', 'C65432', 'Dur desc 1', 'False', '', '12 F' ],
[ '', '', '', '', '', '', '', '', 'Admin 5', 'Admin Desc 5', 'Admin Label 1', 'C345675', '1 mg', 'C65432', 'Dur desc 1', 'False', '', '15 in' ],
]

mock_read = mocker.patch("pandas.read_excel")
Expand Down Expand Up @@ -100,7 +104,7 @@ def test_create(mocker, globals):
"name": "Admin 1",
"label": "Admin Label 1",
"medicalDeviceId": None,
"administrableProductId": None,
"administrableProductId": "pid_4",
"description": "Admin Desc 1",
"duration": {
"id": "Id_3",
Expand Down Expand Up @@ -624,7 +628,7 @@ def test_read_cell_by_name_error(mocker, globals):
mock_error = mocker.patch("usdm_excel.errors_and_logging.errors.Errors.add")
mocked_open = mocker.mock_open(read_data="File")
mocker.patch("builtins.open", mocked_open)
data = [['', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '']]
data = [['', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '']]
mock_read = mocker.patch("pandas.read_excel")
columns = COLUMNS
columns = columns[0:-1]
Expand All @@ -636,3 +640,11 @@ def test_read_cell_by_name_error(mocker, globals):
assert mock_error.call_args[0][2] == None
assert mock_error.call_args[0][3] == "Exception. Error [Failed to detect column(s) 'administrationDurationQuantity' in sheet] while reading sheet 'studyDesignInterventions'. See log for additional details."

def _create_products(factory: Factory, globals: Globals):
std_code =factory.cdisc_code("C70793", "XX1")
items = [
{'name': 'Product 1', 'productDesignation': factory.cdisc_code("C70793", "YYY"), 'sourcing': factory.cdisc_code("C70793", "XXX"), 'administrableDoseForm': factory.alias_code(std_code, [])},
]
for item in items:
instance = factory.item(AdministrableProduct, item)
globals.cross_references.add(item['name'], instance)

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