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Update with master #22

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a15f529
Improve dependencies intro material
liambarnes Jan 9, 2024
91d78f3
Update AU Core dependency, fix terminology page comment tag issue
liambarnes Jan 10, 2024
398693d
Supress non-problematic warnings
liambarnes Jan 10, 2024
9d56b60
Improve QA report readability - Suppress warnings
liambarnes Jan 16, 2024
6e22cac
Improve terminology referencing
liambarnes Jan 16, 2024
459d147
Update publisher/package
liambarnes Jan 18, 2024
dbd380e
Update assembled questionnaire
liambarnes Jan 22, 2024
df9ab34
Fix bulk import script printing out assemble output parameters
fongsean Feb 12, 2024
15dbc8b
build settings artefacts
liambarnes Feb 15, 2024
c9311a9
update forms server endpoint
liambarnes Feb 15, 2024
39f2e24
Fix ObsTobaccoSmokingStatus variable code
liambarnes Mar 26, 2024
8fdc8bd
dates, gender harmony concepts, emergency contact fix, smoking status…
liambarnes Apr 2, 2024
61f8865
alignment changes
liambarnes Apr 3, 2024
04b9086
Merge pull request #23 from aehrc/au-core-alignment
liambarnes Apr 3, 2024
80e92cb
update publisher
liambarnes Apr 3, 2024
834d196
sushi update
liambarnes Apr 3, 2024
5d363fc
remove trailing whitespace from "Section completed" xhtml
liambarnes Apr 3, 2024
5dd36f0
QA issue resolution
liambarnes Apr 4, 2024
dfe1a3c
fix some displays
liambarnes Apr 4, 2024
086e759
Add updated assembled health check questionnaire
liambarnes Apr 4, 2024
ca6f822
Add acceptable canonical url
liambarnes Apr 4, 2024
e0bce7a
improve consistency of internal references of terminology
liambarnes Apr 4, 2024
69e3311
Add updated assembled health check questionnaire
liambarnes Apr 4, 2024
4d520fa
Fix terminology dependency and fhirpath bugs
liambarnes Apr 5, 2024
312f36d
Fix context display enableWhen
liambarnes Apr 5, 2024
3338361
Add copyright
liambarnes Apr 5, 2024
69f690c
Add SCT supplement and associated value sets to support consumer frie…
liambarnes Apr 8, 2024
540c53c
Align displays accurately to SNOMED CT
liambarnes Apr 8, 2024
ca77927
Add updated assembled health check questionnaire
liambarnes Apr 8, 2024
cdc7b6d
Add additional contained value sets to assembly and updated assembled…
liambarnes Apr 9, 2024
2ccc724
remove required
liambarnes Apr 18, 2024
b27af3d
Add encounter launch context
liambarnes Apr 22, 2024
a7a402e
Add updated assembled health check questionnaire
liambarnes Apr 22, 2024
acd19ab
Update licence
liambarnes May 8, 2024
6517a86
Update integration requirements document
liambarnes May 21, 2024
800cdf4
Update smoking status query to use LOINC code
liambarnes May 22, 2024
8565537
Swap medical history value set, update publisher
liambarnes Jul 14, 2024
a8fcb07
Fix terminology referencing
liambarnes Jul 15, 2024
48d6309
update ignoreWarning
liambarnes Jul 15, 2024
c541584
update ignoreWarning
liambarnes Jul 15, 2024
f114f01
update gitignore
liambarnes Jul 25, 2024
ff88236
Delete fsh-generated/fsh-index.json
liambarnes Jul 25, 2024
d2f6641
Delete fsh-generated/fsh-index.txt
liambarnes Jul 25, 2024
bf17f1d
Delete fsh-generated/includes directory
liambarnes Jul 25, 2024
7386fe8
update gitignore
liambarnes Jul 25, 2024
99ff103
Add smart app launch dependency
liambarnes Jul 30, 2024
daa650f
Doctype update to fix build timeout
liambarnes Sep 10, 2024
1345ca9
Fix displays
liambarnes Sep 19, 2024
c29318c
Update ignore warnings
liambarnes Sep 23, 2024
24178e9
Fix terminology metadata
liambarnes Sep 23, 2024
c5f4dde
bump version
liambarnes Sep 23, 2024
6b40b6e
Add placeholder publication request
liambarnes Sep 24, 2024
8a7a8c5
Update LICENSE
liambarnes Oct 1, 2024
2cf5f93
Update tobacco use terminology answer set
liambarnes Nov 29, 2024
f3cc4d1
Update tobacco use terminology answer set
liambarnes Nov 29, 2024
2fe8d9a
Update dependent versions in assembly instructions. Add updated assem…
liambarnes Nov 29, 2024
8fe05a7
Add additional info when error is thrown in bulk-import-ci.py
fongsean Nov 29, 2024
1a52d02
Merge remote-tracking branch 'origin/master'
fongsean Nov 29, 2024
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19 changes: 10 additions & 9 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -1,12 +1,13 @@
bulk-import.py
.DS_Store
Thumbs.db
/assembler
# /fsh-generated
/input-cache
/node_modules
/output
/temp
/template
/.vscode
bulk-import.py
assembler/
fsh-generated/fsh-index.*
fsh-generated/includes/
input-cache/
node_modules/
output/
temp/
template/
.vscode/
fhir.schema.json
572 changes: 371 additions & 201 deletions LICENSE

Large diffs are not rendered by default.

20 changes: 19 additions & 1 deletion bulk-import-ci.py
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,17 @@

HEADERS = {"Content-Type": "application/json"}

# Print out more information if an error occurred
def printErrorAdditionalDetails(e):
print(f"{ERROR_RED}*** Additional error details: ***{END_C}")
if e.response is not None:
print(f"{ERROR_RED}Status Code: {e.response.status_code}{END_C}")
print(f"{ERROR_RED}Reason: {e.response.reason}{END_C}")
print(f"{ERROR_RED}Response Text: {e.response.text}{END_C}")
else:
print(f"{ERROR_RED}No additional error information available.{END_C}")
print()

# Get questionnaire resources from a defined output directory
def getQuestionnairesFromLocalIg():
questionnaires = {}
Expand Down Expand Up @@ -99,10 +110,13 @@ def updateRootAndSubquestionnaires(questionnaires, implementationGuide):
print(
f"{ERROR_RED}ERROR: Fail to find {reference} in local files, questionnaire not updated in server. {END_C}"
)
printErrorAdditionalDetails(e)
except requests.exceptions.HTTPError as e:
print(f"{ERROR_RED}ERROR: HTTP ERROR THROWN:{END_C}", e, '\n')
printErrorAdditionalDetails(e)
except Exception as e:
print(f"{ERROR_RED}ERROR: An error occurred, details:{END_C}", e, '\n')
printErrorAdditionalDetails(e)



Expand All @@ -126,7 +140,6 @@ def assembleQuestionnaire(questionnaires):
f"{OK_GREEN}POST request Questionnaire/$assemble successful at {formsServerEndpoint}: {response.status_code} OK{END_C}"
)
assembleOutputParams = response.json()
print(assembleOutputParams)

# Return bare questionnaire
if assembleOutputParams["resourceType"] == "Questionnaire":
Expand All @@ -143,6 +156,7 @@ def assembleQuestionnaire(questionnaires):
f"{ERROR_RED}ERROR: Unable to retrieve assembled questionnaire from output parameters{END_C}",
e, '\n'
)
printErrorAdditionalDetails(e)

else:
print(
Expand All @@ -151,8 +165,10 @@ def assembleQuestionnaire(questionnaires):

except requests.exceptions.HTTPError as e:
print(f"{ERROR_RED}ERROR: HTTP ERROR THROWN:{END_C}",e, '\n')
printErrorAdditionalDetails(e)
except Exception as e:
print(f"{ERROR_RED}ERROR: An error occurred, details:", e, '\n')
printErrorAdditionalDetails(e)

return None

Expand Down Expand Up @@ -183,8 +199,10 @@ def updateAssembledQuestionnaire(questionnaire):

except requests.exceptions.HTTPError as e:
print(f"{ERROR_RED}ERROR: HTTP ERROR THROWN:{END_C}",e, '\n')
printErrorAdditionalDetails(e)
except Exception as e:
print(f"{ERROR_RED}ERROR: An error occurred, details:", e, '\n')
printErrorAdditionalDetails(e)


# Main function
Expand Down
53 changes: 0 additions & 53 deletions fsh-generated/includes/fsh-link-references.md

This file was deleted.

54 changes: 0 additions & 54 deletions fsh-generated/includes/menu.xml

This file was deleted.

58 changes: 58 additions & 0 deletions fsh-generated/resources/CodeSystem-HealthChecksSCTSupplement.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,58 @@
{
"resourceType": "CodeSystem",
"status": "draft",
"content": "supplement",
"name": "HealthChecksSCTSupplement",
"id": "HealthChecksSCTSupplement",
"title": "SNOMED CT Supplement for Aboriginal and Torres Strait Islander Health Check",
"description": "The SNOMED CT Supplement for Aboriginal and Torres Strait Islander Health Check code system supplement defines consumer friendly terms for use in the health check Questionnaire.",
"url": "https://smartforms.csiro.au/ig/CodeSystem/HealthChecksSCTSupplement",
"concept": [
{
"code": "736595007",
"display": "Declined"
},
{
"code": "171154002",
"display": "Not required"
},
{
"code": "171155001",
"display": "Up to date"
},
{
"code": "48031000119106",
"display": "Quit >12 months"
},
{
"code": "735128000",
"display": "Quit <12 months"
},
{
"code": "266919005",
"display": "Never smoked"
},
{
"code": "77176002",
"display": "Current smoker"
},
{
"code": "8517006",
"display": "Ex-smoker"
},
{
"code": "16090371000119103",
"display": "Exposure to second hand tobacco smoke"
},
{
"code": "394872000",
"display": "Wants to quit"
},
{
"code": "713914004",
"display": "Other tobacco use"
}
],
"experimental": false,
"supplements": "http://snomed.info/sct|http://snomed.info/sct/32506021000036107"
}
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