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Merged
jli755 merged 5 commits into from
Jul 4, 2025
Merged

issue-63-create-generalised-version-of-validate_removal_of_references #64

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f660822
Simplified example code for removing elements from items
ollylucl Jun 19, 2025
cb77215
move code
ollylucl Jun 19, 2025
a837a09
address linter error in github
ollylucl Jun 19, 2025
e348e2d
add package name to lines executing function
ollylucl Jun 19, 2025
d2eb180
Include instructions for how to run method as comments, not as actual
ollylucl Jun 19, 2025
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47 changes: 18 additions & 29 deletions examples/remove_elements_from_items.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
6. Verifying that the removal of the references has been successful.
"""

from lib.utility import (
from examples.lib.utility import (
update_repository,
get_elements_of_type,
remove_elements_from_item
Expand All @@ -32,15 +32,11 @@
# use the most up to date version of the study/series!
search_sets = [{"agencyId": "uk.cls.mcs",
"identifier": "0d8a7220-c61b-4542-967d-a40cb5aca430",
"version": "60"}]
"version": "58"}]

allItemsInOneQuery = C.search_items([], SearchSets=search_sets)['Results']
studies=C.search_items([C.item_code('Study')], SearchSets=search_sets)['Results']

studies = [x for x in allItemsInOneQuery if x['ItemType']
== C.item_code('Study')]

dataCollections = [x for x in allItemsInOneQuery if x['ItemType']
== C.item_code('Data Collection')]
dataCollections=C.search_items([C.item_code('Data Collection')], SearchSets=search_sets)['Results']

dataCollectionItems = []
updatedDataCollections = []
Expand Down Expand Up @@ -96,10 +92,15 @@
#
# Execute this code by making sure you have defined the 'validate_removal_of_references' and
# 'count_elements_in_items' methods in your Python interpreter environment (e.g. by copying
# and pasting the methods code below into your Python interpreter) and typing:
# and pasting the methods below into your Python interpreter) and typing commands such as
# the ones below, which check that, for example, the 'InstrumentReference' elements that were
# present in the objects in the dataCollectionItems array are not present in the objects in the
# updatedDataCollections array:
#
# validate_removal_of_references(dataCollectionItems, updatedDataCollections, studyItems,
# updatedStudies)
# validate_removal_of_references(dataCollectionItems, updatedDataCollections, "InstrumentReference")
# validate_removal_of_references(dataCollectionItems, updatedDataCollections, "QuestionSchemeReference")
# validate_removal_of_references(studyItems, updatedStudies, "PhysicalInstanceReference")
# validate_removal_of_references(studyItems, updatedStudies, "RequiredResourcePackages")

def count_elements_in_items(items, elementTagname):
"""Given a list of items and the tag name of an element, this function counts
Expand All @@ -109,21 +110,9 @@ def count_elements_in_items(items, elementTagname):
elementCount += len(get_elements_of_type(item, elementTagname))
return elementCount

def validate_removal_of_references(dataCollectionItems,
updatedDataCollections, studyItems, updatedStudies):
instrumentRefsBefore = count_elements_in_items(dataCollectionItems, "InstrumentReference")
print(f"Number of instrument references in data collections before removal: {instrumentRefsBefore}")
instrumentRefsAfter = count_elements_in_items([x['Item'] for x in updatedDataCollections], "InstrumentReference")
print(f"Number of instrument references in data collections after removal: {instrumentRefsAfter}")
questionSchemeRefsBefore = count_elements_in_items(dataCollectionItems, "QuestionSchemeReference")
print(f"Number of question scheme references in data collections before removal: {questionSchemeRefsBefore}")
questionSchemeRefsAfter = count_elements_in_items([x['Item'] for x in updatedDataCollections], "QuestionSchemeReference")
print(f"Number of question scheme references in data collections after removal: {questionSchemeRefsAfter}")
physicalInstanceRefsBefore = count_elements_in_items(studyItems, "PhysicalInstanceReference")
print(f"Number of physical instance references in studies before removal: {physicalInstanceRefsBefore}")
physicalInstanceRefsAfter = count_elements_in_items([x['Item'] for x in updatedStudies], "PhysicalInstanceReference")
print(f"Number of physical instance references in studies after removal: {physicalInstanceRefsAfter}")
requiredResourcePackagesBefore = count_elements_in_items(studyItems, "RequiredResourcePackages")
print(f"Number of required resource packages in studies before removal: {requiredResourcePackagesBefore}")
requiredResourcePackagesAfter = count_elements_in_items([x['Item'] for x in updatedStudies], "RequiredResourcePackages")
print(f"Number of required resource packages in studies after removal: {requiredResourcePackagesAfter}")
def validate_removal_of_references(itemsBefore, itemsAfter, referenceTagName):
referencesBefore = count_elements_in_items(itemsBefore, referenceTagName)
itemTypes = set([C.item_code_inv(x['ItemType']) for x in itemsAfter])
print(f"Number of {referenceTagName} elements in {itemTypes} items before removal: {referencesBefore}")
referencesAfter = count_elements_in_items([x['Item'] for x in itemsAfter], "VariableReference")
print(f"Number of {referenceTagName} elements in {itemTypes} items after removal: {referencesAfter}")