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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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168 changes: 152 additions & 16 deletions fsh-generated/fsh-index.json
View file
Open in desktop
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-GRU.json",
"fshName": "GRU",
"fshType": "Instance",
"fshFile": "examples/participant.fsh",
"startLine": 88,
"endLine": 101
},
{
"outputFile": "Consent-HMB.json",
"fshName": "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": 116,
"endLine": 122
},
{
"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": 124,
"endLine": 131
},
{
"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": 133,
"endLine": 145
},
{
"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": 101,
"endLine": 112
},
{
"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
33 changes: 25 additions & 8 deletions fsh-generated/fsh-index.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,11 @@ CodeSystem-collection-type.json CollectionType
CodeSystem-ncpi.json Ncpi CodeSystem terminologies/ncpi.fsh 6 - 34
CodeSystem-research-data-access-code.json ResearchDataAccessCode CodeSystem modules/research-accesss-policy.fsh 6 - 22
CodeSystem-research-data-access-type.json ResearchDataAccessType CodeSystem modules/research-accesss-policy.fsh 33 - 44
CodeSystem-research-data-date-of-birth-method.json ResearchDataDateOfBirthMethod CodeSystem modules/participant.fsh 26 - 37
CodeSystem-research-data-date-of-birth-method.json ResearchDataDateOfBirthMethod CodeSystem modules/participant.fsh 18 - 29
CodeSystem-study-name-type.json StudyNameType CodeSystem modules/research-study.fsh 99 - 110
CodeSystem-study-personnel-role.json StudyPersonnelRole CodeSystem modules/research-study.fsh 120 - 129
Consent-GRU.json GRU Instance examples/participant.fsh 88 - 101
Consent-HMB.json HMB Instance examples/participant.fsh 178 - 191
Consent-hmb-irb-npu-consent.json hmb-irb-npu-consent Instance examples/ResearchStudy-BH-CMG.fsh 117 - 133
Consent-hmb-npu-consent.json hmb-npu-consent Instance examples/ResearchStudy-BH-CMG.fsh 71 - 86
Consent-kf-gru-dac-consent.json kf-gru-dac-consent Instance examples/ResearchStudy-CBTN.fsh 105 - 118
Expand All @@ -19,10 +21,17 @@ List-ncpi-research-collection-cmg.json ncpi-research-
List-ncpi-research-collection-kfx01.json ncpi-research-collection-kfx01 Instance examples/ResearchStudy-CBTN.fsh 236 - 246
List-ncpi-research-collection-pbta.json ncpi-research-collection-pbta Instance examples/ResearchStudy-CBTN.fsh 222 - 234
Organization-kf-research-study-organization-chop.json kf-research-study-organization-chop Instance examples/ResearchStudy-CBTN.fsh 4 - 11
Patient-PT-KZG2CZ95.json PT-KZG2CZ95 Instance examples/participant.fsh 2 - 41
Patient-6812345.json 6812345 Instance examples/participant.fsh 222 - 255
Patient-PT-005B7CZ4.json PT-005B7CZ4 Instance examples/participant.fsh 132 - 164
Patient-PT-KZG2CZ95.json PT-KZG2CZ95 Instance examples/participant.fsh 15 - 54
Person-cbtn-example-person.json cbtn-example-person Instance examples/participant.fsh 77 - 86
Person-emerge-example-person.json emerge-example-person Instance examples/participant.fsh 257 - 266
Person-pcgc-example-person.json pcgc-example-person Instance examples/participant.fsh 167 - 176
PractitionerRole-kf-research-study-personnel-role-op-lead.json kf-research-study-personnel-role-op-lead Instance examples/ResearchStudy-CBTN.fsh 29 - 35
PractitionerRole-kf-research-study-personnel-role-pi-x01.json kf-research-study-personnel-role-pi-x01 Instance examples/ResearchStudy-CBTN.fsh 13 - 19
PractitionerRole-kf-research-study-personnel-role-pi.json kf-research-study-personnel-role-pi Instance examples/ResearchStudy-CBTN.fsh 21 - 27
ResearchStudy-SD-BHJXBDQK.json SD-BHJXBDQK Instance examples/participant.fsh 103 - 116
ResearchStudy-SD-PREASA7S.json SD-PREASA7S Instance examples/participant.fsh 193 - 206
ResearchStudy-cmg-research-study-bhcmg.json cmg-research-study-bhcmg Instance examples/ResearchStudy-BH-CMG.fsh 16 - 67
ResearchStudy-cmg-research-study-subject-cmg-hmb-npu.json cmg-research-study-subject-cmg-hmb-npu Instance examples/ResearchStudy-BH-CMG.fsh 102 - 115
ResearchStudy-cmg-research-study-subject-cmg-irb-hmb-npu.json cmg-research-study-subject-cmg-irb-hmb-npu Instance examples/ResearchStudy-BH-CMG.fsh 148 - 161
Expand All @@ -31,22 +40,30 @@ ResearchStudy-kf-research-study-subject-gru-dac.json kf-research-st
ResearchStudy-kf-research-study-subject-gru-dbgap.json kf-research-study-subject-gru-dbgap Instance examples/ResearchStudy-CBTN.fsh 150 - 163
ResearchStudy-kf-research-study-subject-gsr-allowed.json kf-research-study-subject-gsr-allowed Instance examples/ResearchStudy-CBTN.fsh 178 - 191
ResearchStudy-kf-research-study-subject-registered.json kf-research-study-subject-registered Instance examples/ResearchStudy-CBTN.fsh 206 - 219
StructureDefinition-SharedDataModelPerson.json CdmPerson Logical modules/participant.fsh 18 - 23
ResearchStudy-phv00407460.v2.json phv00407460.v2 Instance examples/participant.fsh 270 - 283
ResearchSubject-cbtn-example-participantstudy.json cbtn-example-participantstudy Instance examples/participant.fsh 118 - 126
ResearchSubject-emerge-example-participantstudy.json emerge-example-participantstudy Instance examples/participant.fsh 285 - 293
ResearchSubject-pcgc-example-participantstudy.json pcgc-example-participantstudy Instance examples/participant.fsh 208 - 216
StructureDefinition-SharedDataModelPerson.json CdmPerson Logical modules/participant.fsh 93 - 98
StructureDefinition-SharedDataModelResearchCollection.json CdmResearchCollection Logical modules/research-collection.fsh 39 - 48
StructureDefinition-SharedDataModelResearchDataAccessPolicy.json CdmResearchDataAccessPolicy Logical modules/research-accesss-policy.fsh 113 - 120
StructureDefinition-SharedDataModelResearchParticipant.json CdmResearchParticipant Logical modules/participant.fsh 3 - 16
StructureDefinition-SharedDataModelResearchStudy.json CdmResearchStudy Logical modules/research-study.fsh 138 - 168
StructureDefinition-SharedDataModelStudyParticipant.json CdmStudyParticipant Logical modules/participant.fsh 116 - 122
StructureDefinition-access-policy-description.json AccessPolicyDescription Extension modules/research-accesss-policy.fsh 83 - 90
StructureDefinition-access-policy.json AccessPolicy Extension modules/participant.fsh 124 - 131
StructureDefinition-access-type.json AccessType Extension modules/research-accesss-policy.fsh 75 - 81
StructureDefinition-label-extension.json Label Extension extensions/Label.fsh 1 - 13
StructureDefinition-ncpi-participant.json NcpiParticipant Profile modules/participant.fsh 70 - 95
StructureDefinition-ncpi-Study-Participant.json NcpiStudyParticipant Profile modules/participant.fsh 133 - 145
StructureDefinition-ncpi-participant.json NcpiParticipant Profile modules/participant.fsh 62 - 87
StructureDefinition-ncpi-person.json NcpiPerson Profile modules/participant.fsh 101 - 112
StructureDefinition-ncpi-research-access-policy.json NcpiResearchAccessPolicy Profile modules/research-accesss-policy.fsh 92 - 110
StructureDefinition-ncpi-research-collection.json NcpiResearchCollection Profile modules/research-collection.fsh 20 - 37
StructureDefinition-ncpi-research-study.json NcpiResearchStudy Profile modules/research-study.fsh 60 - 86
StructureDefinition-research-age-at-last-vital-status.json AgeAtLastVitalStatus Extension modules/participant.fsh 61 - 68
StructureDefinition-research-date-of-birth-method.json ResearchDateOfBirthMethod Extension modules/participant.fsh 53 - 59
StructureDefinition-research-age-at-last-vital-status.json AgeAtLastVitalStatus Extension modules/participant.fsh 53 - 60
StructureDefinition-research-date-of-birth-method.json ResearchDateOfBirthMethod Extension modules/participant.fsh 45 - 51
StructureDefinition-research-disease-use-limitation.json ResearchDiseaseUseLimitation Extension modules/research-accesss-policy.fsh 67 - 73
StructureDefinition-research-population.json ResearchPopulation Extension modules/participant.fsh 45 - 50
StructureDefinition-research-population.json ResearchPopulation Extension modules/participant.fsh 37 - 42
StructureDefinition-research-study-acknowledgement.json ResearchStudyAcknowledgement Extension modules/research-study.fsh 22 - 29
StructureDefinition-research-study-associated-party.json ResearchStudyAssociatedParty Extension modules/research-study.fsh 31 - 57
StructureDefinition-research-study-design.json ResearchStudyDesign Extension modules/research-study.fsh 7 - 13
Expand All @@ -59,6 +76,6 @@ ValueSet-collection-type-vs.json CollectionType
ValueSet-mesh-terms.json MeshTerms ValueSet modules/research-accesss-policy.fsh 54 - 60
ValueSet-research-data-access-code-vs.json ResearchDataAccessCodeVS ValueSet modules/research-accesss-policy.fsh 25 - 30
ValueSet-research-data-access-type-vs.json ResearchDataAccessTypeVS ValueSet modules/research-accesss-policy.fsh 47 - 52
ValueSet-research-data-date-of-birth-method-vs.json ResearchDataDateOfBirthMethodVS ValueSet modules/participant.fsh 39 - 43
ValueSet-research-data-date-of-birth-method-vs.json ResearchDataDateOfBirthMethodVS ValueSet modules/participant.fsh 31 - 35
ValueSet-study-name-type-vs.json StudyNameTypeVS ValueSet modules/research-study.fsh 113 - 118
ValueSet-study-personnel-role-vs.json StudyPersonnelRoleVS ValueSet modules/research-study.fsh 131 - 136
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