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Add the Person and StudyParticipant profiles to the Participant module #28

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merged 7 commits into from
Jul 30, 2024
Merged

Add the Person and StudyParticipant profiles to the Participant module #28

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8ded971
:sparkles: Add Person and Study Participant Modules
Jul 19, 2024
9914bbc
:construction: Add Stub Studies and Consents to the Participant Examples
Jul 22, 2024
a5a2819
:construction: Update Person and StudyParticipant pagecontent
Jul 22, 2024
68e4d50
:construction: Revert changes to .sh and .bat files
Jul 29, 2024
66a96b1
:construction: Remove gencontinuous files
Jul 29, 2024
6a273d2
:construction: Make suggested changes
Jul 29, 2024
e695b21
:construction: Suggested change to NcpiPerson link
Jul 29, 2024
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2 changes: 2 additions & 0 deletions _gencontinuous.bat
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Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
@ECHO OFF
CALL ./_genonce.bat -watch
2 changes: 2 additions & 0 deletions _gencontinuous.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
#!/bin/bash
./_genonce.sh -watch
7 changes: 2 additions & 5 deletions _genonce.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -12,21 +12,18 @@ else
txoption="-tx n/a"
fi

# We are getting warnings about local code systems, so I'm turning it off for now
txoption=""
echo "$txoption"

export JAVA_TOOL_OPTIONS="$JAVA_TOOL_OPTIONS -Dfile.encoding=UTF-8"

publisher=$input_cache_path/$publisher_jar
if test -f "$publisher"; then
# For folks working on headless machines who don't want to bother with X11
java -Djava.awt.headless=true -jar $publisher -ig . $txoption $*
java -jar $publisher -ig . $txoption $*

else
publisher=../$publisher_jar
if test -f "$publisher"; then
java -Djava.awt.headless=true -jar $publisher -ig . $txoption $*
java -jar $publisher -ig . $txoption $*
else
echo IG Publisher NOT FOUND in input-cache or parent folder. Please run _updatePublisher. Aborting...
fi
Expand Down
168 changes: 152 additions & 16 deletions fsh-generated/fsh-index.json
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Original file line number Diff line number Diff line change
Expand Up @@ -36,8 +36,8 @@
"fshName": "ResearchDataDateOfBirthMethod",
"fshType": "CodeSystem",
"fshFile": "modules/participant.fsh",
"startLine": 26,
"endLine": 37
"startLine": 18,
"endLine": 29
},
{
"outputFile": "CodeSystem-study-name-type.json",
Expand All @@ -55,6 +55,22 @@
"startLine": 120,
"endLine": 129
},
{
"outputFile": "Consent-AP-GRU.json",
"fshName": "AP-GRU",
"fshType": "Instance",
"fshFile": "examples/participant.fsh",
"startLine": 88,
"endLine": 101
},
{
"outputFile": "Consent-AP-HMB.json",
"fshName": "AP-HMB",
"fshType": "Instance",
"fshFile": "examples/participant.fsh",
"startLine": 178,
"endLine": 191
},
{
"outputFile": "Consent-hmb-irb-npu-consent.json",
"fshName": "hmb-irb-npu-consent",
Expand Down Expand Up @@ -159,13 +175,53 @@
"startLine": 4,
"endLine": 11
},
{
"outputFile": "Patient-6812345.json",
"fshName": "6812345",
"fshType": "Instance",
"fshFile": "examples/participant.fsh",
"startLine": 222,
"endLine": 255
},
{
"outputFile": "Patient-PT-005B7CZ4.json",
"fshName": "PT-005B7CZ4",
"fshType": "Instance",
"fshFile": "examples/participant.fsh",
"startLine": 132,
"endLine": 164
},
{
"outputFile": "Patient-PT-KZG2CZ95.json",
"fshName": "PT-KZG2CZ95",
"fshType": "Instance",
"fshFile": "examples/participant.fsh",
"startLine": 2,
"endLine": 41
"startLine": 15,
"endLine": 54
},
{
"outputFile": "Person-cbtn-example-person.json",
"fshName": "cbtn-example-person",
"fshType": "Instance",
"fshFile": "examples/participant.fsh",
"startLine": 77,
"endLine": 86
},
{
"outputFile": "Person-emerge-example-person.json",
"fshName": "emerge-example-person",
"fshType": "Instance",
"fshFile": "examples/participant.fsh",
"startLine": 257,
"endLine": 266
},
{
"outputFile": "Person-pcgc-example-person.json",
"fshName": "pcgc-example-person",
"fshType": "Instance",
"fshFile": "examples/participant.fsh",
"startLine": 167,
"endLine": 176
},
{
"outputFile": "PractitionerRole-kf-research-study-personnel-role-op-lead.json",
Expand All @@ -191,6 +247,22 @@
"startLine": 21,
"endLine": 27
},
{
"outputFile": "ResearchStudy-SD-BHJXBDQK.json",
"fshName": "SD-BHJXBDQK",
"fshType": "Instance",
"fshFile": "examples/participant.fsh",
"startLine": 103,
"endLine": 116
},
{
"outputFile": "ResearchStudy-SD-PREASA7S.json",
"fshName": "SD-PREASA7S",
"fshType": "Instance",
"fshFile": "examples/participant.fsh",
"startLine": 193,
"endLine": 206
},
{
"outputFile": "ResearchStudy-cmg-research-study-bhcmg.json",
"fshName": "cmg-research-study-bhcmg",
Expand Down Expand Up @@ -255,13 +327,45 @@
"startLine": 206,
"endLine": 219
},
{
"outputFile": "ResearchStudy-phv00407460.v2.json",
"fshName": "phv00407460.v2",
"fshType": "Instance",
"fshFile": "examples/participant.fsh",
"startLine": 270,
"endLine": 283
},
{
"outputFile": "ResearchSubject-cbtn-example-participantstudy.json",
"fshName": "cbtn-example-participantstudy",
"fshType": "Instance",
"fshFile": "examples/participant.fsh",
"startLine": 118,
"endLine": 126
},
{
"outputFile": "ResearchSubject-emerge-example-participantstudy.json",
"fshName": "emerge-example-participantstudy",
"fshType": "Instance",
"fshFile": "examples/participant.fsh",
"startLine": 285,
"endLine": 293
},
{
"outputFile": "ResearchSubject-pcgc-example-participantstudy.json",
"fshName": "pcgc-example-participantstudy",
"fshType": "Instance",
"fshFile": "examples/participant.fsh",
"startLine": 208,
"endLine": 216
},
{
"outputFile": "StructureDefinition-SharedDataModelPerson.json",
"fshName": "CdmPerson",
"fshType": "Logical",
"fshFile": "modules/participant.fsh",
"startLine": 18,
"endLine": 23
"startLine": 93,
"endLine": 98
},
{
"outputFile": "StructureDefinition-SharedDataModelResearchCollection.json",
Expand Down Expand Up @@ -295,6 +399,14 @@
"startLine": 138,
"endLine": 168
},
{
"outputFile": "StructureDefinition-SharedDataModelStudyParticipant.json",
"fshName": "CdmStudyParticipant",
"fshType": "Logical",
"fshFile": "modules/participant.fsh",
"startLine": 124,
"endLine": 130
},
{
"outputFile": "StructureDefinition-access-policy-description.json",
"fshName": "AccessPolicyDescription",
Expand All @@ -303,6 +415,14 @@
"startLine": 83,
"endLine": 90
},
{
"outputFile": "StructureDefinition-access-policy.json",
"fshName": "AccessPolicy",
"fshType": "Extension",
"fshFile": "modules/participant.fsh",
"startLine": 100,
"endLine": 107
},
{
"outputFile": "StructureDefinition-access-type.json",
"fshName": "AccessType",
Expand All @@ -319,13 +439,29 @@
"startLine": 1,
"endLine": 13
},
{
"outputFile": "StructureDefinition-ncpi-Study-Participant.json",
"fshName": "NcpiStudyParticipant",
"fshType": "Profile",
"fshFile": "modules/participant.fsh",
"startLine": 132,
"endLine": 144
},
{
"outputFile": "StructureDefinition-ncpi-participant.json",
"fshName": "NcpiParticipant",
"fshType": "Profile",
"fshFile": "modules/participant.fsh",
"startLine": 70,
"endLine": 95
"startLine": 62,
"endLine": 87
},
{
"outputFile": "StructureDefinition-ncpi-person.json",
"fshName": "NcpiPerson",
"fshType": "Profile",
"fshFile": "modules/participant.fsh",
"startLine": 109,
"endLine": 119
},
{
"outputFile": "StructureDefinition-ncpi-research-access-policy.json",
Expand Down Expand Up @@ -356,16 +492,16 @@
"fshName": "AgeAtLastVitalStatus",
"fshType": "Extension",
"fshFile": "modules/participant.fsh",
"startLine": 61,
"endLine": 68
"startLine": 53,
"endLine": 60
},
{
"outputFile": "StructureDefinition-research-date-of-birth-method.json",
"fshName": "ResearchDateOfBirthMethod",
"fshType": "Extension",
"fshFile": "modules/participant.fsh",
"startLine": 53,
"endLine": 59
"startLine": 45,
"endLine": 51
},
{
"outputFile": "StructureDefinition-research-disease-use-limitation.json",
Expand All @@ -380,8 +516,8 @@
"fshName": "ResearchPopulation",
"fshType": "Extension",
"fshFile": "modules/participant.fsh",
"startLine": 45,
"endLine": 50
"startLine": 37,
"endLine": 42
},
{
"outputFile": "StructureDefinition-research-study-acknowledgement.json",
Expand Down Expand Up @@ -484,8 +620,8 @@
"fshName": "ResearchDataDateOfBirthMethodVS",
"fshType": "ValueSet",
"fshFile": "modules/participant.fsh",
"startLine": 39,
"endLine": 43
"startLine": 31,
"endLine": 35
},
{
"outputFile": "ValueSet-study-name-type-vs.json",
Expand Down
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