From 9e3069f70afd50974c2c84c26eba5be715ca02a3 Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 7 Jan 2026 13:44:01 -0500 Subject: [PATCH 01/11] Added defaultConditionId to ScheduledActivityInstances --- src/soa_builder/web/routers/instances.py | 10 +++++++- src/soa_builder/web/templates/edit.html | 22 ++++++++--------- src/soa_builder/web/templates/instances.html | 24 ++++++++++++++----- .../web/templates/schedule_timelines.html | 3 ++- src/soa_builder/web/templates/timings.html | 2 +- 5 files changed, 41 insertions(+), 20 deletions(-) diff --git a/src/soa_builder/web/routers/instances.py b/src/soa_builder/web/routers/instances.py index c699ecc..5c79c11 100644 --- a/src/soa_builder/web/routers/instances.py +++ b/src/soa_builder/web/routers/instances.py @@ -9,7 +9,13 @@ from ..audit import _record_instance_audit from ..db import _connect from ..schemas import InstanceCreate, InstanceUpdate -from ..utils import soa_exists, get_encounter_id, get_epoch_uid, get_schedule_timeline +from ..utils import ( + soa_exists, + get_encounter_id, + get_epoch_uid, + get_schedule_timeline, + get_scheduled_activity_instance, +) router = APIRouter() logger = logging.getLogger("soa_builder.web.routers.instances") @@ -67,6 +73,7 @@ def ui_list_instances(request: Request, soa_id: int): encounter_options = get_encounter_id(soa_id) epoch_options = get_epoch_uid(soa_id) schedule_timelines_options = get_schedule_timeline(soa_id) + instance_options = get_scheduled_activity_instance(soa_id) return templates.TemplateResponse( "instances.html", @@ -77,6 +84,7 @@ def ui_list_instances(request: Request, soa_id: int): "encounter_options": encounter_options, "epoch_options": epoch_options, "schedule_timelines_options": schedule_timelines_options, + "instance_options": instance_options, }, ) diff --git a/src/soa_builder/web/templates/edit.html b/src/soa_builder/web/templates/edit.html index 2b31e52..e9bfa37 100644 --- a/src/soa_builder/web/templates/edit.html +++ b/src/soa_builder/web/templates/edit.html @@ -83,7 +83,7 @@

Editing SoA {{ soa_id }}

- Visits ({{ visits|length }}) (drag to reorder) + Visits/Encounters ({{ visits|length }}) (drag to reorder)
    {% for v in visits %}
  • @@ -93,7 +93,7 @@

    Editing SoA {{ soa_id }}

    - + {% for opt in protocol_terminology_C174222 %} {% set text = (opt.cdisc_submission_value or '') %} {% set td = (arm.type_display or '') %} @@ -314,7 +314,7 @@

    Editing SoA {{ soa_id }}

    {# Type selection from ddf terminology C188727 #} {% if ddf_terminology_C188727 %} +
@@ -43,7 +48,7 @@

Scheduled Activity Instances for SoA {{ soa_id }}

@@ -52,7 +57,7 @@

Scheduled Activity Instances for SoA {{ soa_id }}

@@ -78,11 +83,18 @@

Scheduled Activity Instances for SoA {{ soa_id }}

{% for i in instances or [] %} - {{ i.instance_uid }} + {{ i.instance_uid }} - + + + diff --git a/src/soa_builder/web/templates/timings.html b/src/soa_builder/web/templates/timings.html index 77823c7..a47eceb 100644 --- a/src/soa_builder/web/templates/timings.html +++ b/src/soa_builder/web/templates/timings.html @@ -107,7 +107,7 @@

Timings for SoA {{ soa_id }}

{% for t in timings %} - {{ t.timing_uid }} + {{ t.timing_uid }} From 05fdb893985d8a0b4239d347b0844fbc3ec378f6 Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Wed, 7 Jan 2026 14:00:21 -0500 Subject: [PATCH 02/11] No longer set epoch in visit/encounter --- src/soa_builder/web/templates/edit.html | 20 +- .../web/templates/edit_backup.html | 642 ++++++++++++++++++ 2 files changed, 644 insertions(+), 18 deletions(-) create mode 100644 src/soa_builder/web/templates/edit_backup.html diff --git a/src/soa_builder/web/templates/edit.html b/src/soa_builder/web/templates/edit.html index e9bfa37..7554e7f 100644 --- a/src/soa_builder/web/templates/edit.html +++ b/src/soa_builder/web/templates/edit.html @@ -89,18 +89,7 @@

Editing SoA {{ soa_id }}

  • {{ v.order_index }}. {{ v.name }} - {% if epochs %} - - - - - {% endif %} - {% if timings %} + {% if timings %}
    - {% if epochs %} - - {% endif %} +
    diff --git a/src/soa_builder/web/templates/edit_backup.html b/src/soa_builder/web/templates/edit_backup.html new file mode 100644 index 0000000..e9bfa37 --- /dev/null +++ b/src/soa_builder/web/templates/edit_backup.html @@ -0,0 +1,642 @@ +{% extends 'base.html' %} +{% block content %} +

    Editing SoA {{ soa_id }}

    +
    + Study Metadata +
    +
    + + +
    +
    + + +
    +
    + + +
    +
    + + Study ID must be unique and cannot be cleared once set. Other fields may be left blank to clear. +
    +
    +
    +
    +
    +
    + + +
    +
    +
    + Count: {{ freeze_count }} + {% if last_frozen_at %} • Last: {{ last_frozen_at }}{% endif %} +
    +
    + {% if freezes %} +
    + Versions: + {% for f in freezes %} +
    + {{ f.version_label }} + +
    + {% endfor %} +
    +
    + + + Rollback Audit XLSX + Reorder Audit XLSX + Reorder CSV +
    +
    + Diff: + + + +
    + {% else %} +
    No versions frozen yet.
    + {% endif %} +
    + +
    +
    + +
    +
    + Last fetch: + {% if concepts_last_fetch_relative %} + {{ concepts_last_fetch_relative }} + {% else %} + n/a + {% endif %} +
    + (forces remote re-fetch & cache reset) +
    +
    +
    +
    + Visits/Encounters ({{ visits|length }}) (drag to reorder) +
      + {% for v in visits %} +
    • + {{ v.order_index }}. {{ v.name }} + + {% if epochs %} +
      + + +
      + {% endif %} + {% if timings %} +
      + + +
      + {% endif %} + {% if transition_rules %} +
      + + +
      +
      + + +
      + {% endif %} + +
      + + + + +
      +
      + + +
      +
      +
    • + {% endfor %} +
    +
    + + + + {% if epochs %} + + {% endif %} + +
    +
    +
    + Activities ({{ activities|length }}) (drag to reorder) +
      + {% for a in activities %} +
    • + {{ a.order_index }}. {{ a.name }} + +
      + + + + + +
      +
      + + +
      +
      +
    • + {% endfor %} +
    +
    + + + + +
    +
    + +
    + Epochs ({{ epochs|length }}) (drag to reorder) +
      + {% for e in epochs %} +
    • + {{ e.order_index }}. {{ e.name }} + +
      + + + + + + +
      +
      + + +
      +
      +
    • + {% endfor %} +
    +
    + + + + + +
    +
    +
    + Elements ({{ elements|length }}) (drag to reorder) +
      + {% for el in elements %} +
    • + {{ el.order_index }}. {% if el.label %}{{ el.label }}{% else %}{{ el.name }}{% endif %} + + {% if transition_rules %} +
      + + +
      +
      + + +
      + {% endif %} +
      + + + + + +
      +
      + + +
      +
      +
    • + {% endfor %} +
    +
    + + + + + +
    +
    +
    + Arms ({{ arms|length }}) (drag to reorder) +
      + {% for arm in arms %} +
    • + {{ arm.order_index }}. {% if arm.label %}{{ arm.label }}{% else %}{{ arm.name }}{% endif %} + +
      + + + + + {# Type selection from protocol terminology C174222 #} + {% if protocol_terminology_C174222 %} + + {% endif %} + {# Type selection from ddf terminology C188727 #} + {% if ddf_terminology_C188727 %} + + {% endif %} + +
      +
      + + +
      +
      +
    • + {% endfor %} +
    +
    + + + + {% if protocol_terminology_C174222 %} + + {% endif %} + {% if ddf_terminology_C188727 %} + + {% endif %} + +
    +
    +
    + Study Cells ({{ study_cells|length }}) +
    +
    + + +
    +
    + + +
    +
    + + + Select one or more elements (Cmd/Ctrl+Click). +
    +
    + +
    +
    +
    + + + + + + + + + {% for sc in study_cells %} + + + + + + + + {% else %} + + {% endfor %} +
    UIDArmEpochElementActions
    {{ sc.study_cell_uid }} + {% set arm_match = arms | selectattr('arm_uid', 'equalto', sc.arm_uid) | list %} + {% if arm_match and arm_match[0] and arm_match[0].name %} + {{ arm_match[0].name }} + {% else %} + {{ sc.arm_uid }} + {% endif %} + {{ sc.epoch_name or sc.epoch_uid }}{{ sc.element_name or sc.element_uid }} +
    + + +
    +
    No study cells yet.
    +
    +
    +
    + Transition Rules ({{ transition_rules|length }}) +
      + {% for rule in transition_rules %} +
    • + {{ rule.order_index }}. {% if rule.label %}{{ rule.label }}{% else %}{{ rule.name }}{% endif %} + +
      + + + + + + +
      +
      + + +
      +
      +
    • + {% endfor %} +
    +
    + + + + + +
    +
    +
    + +
    +
    +

    Matrix

    + + + + + {% for v in visits %} + + {% endfor %} + + {% for a in activities %} + + + {% set concepts_list = activity_concepts.get(a.id, []) %} + {% set selected_list = concepts_list %} + {% set selected_codes = concepts_list | map(attribute='code') | list %} + {% set activity_id = a.id %} + {% include 'concepts_cell.html' %} + {% for v in visits %} + {% set raw_status = cell_map.get((v.id, a.id), '') %} + {% set display = 'X' if raw_status == 'X' else '' %} + + {% endfor %} + + {% endfor %} +
    ActivityConcepts +
    {{ v.name }}
    +
    Encounter: {{ v.name }}
    + {% if v.epoch_id %} + {% set ep = (epochs | selectattr('id','equalto', v.epoch_id) | list) %} + {% if ep and ep[0] %}
    Epoch: {{ ep[0].name }}
    {% endif %} + {% endif %} +
    {{ a.name }}{{ display }}
    +

    Generate Normalized Summary (JSON)

    + + + +{% endblock %} From 1eee60ba40e23570cc0df9b5a76916248d2d3755 Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Thu, 8 Jan 2026 15:37:05 -0500 Subject: [PATCH 03/11] Matrix uses activities as row headers and scheduledActivityInstances (instances) as column headers --- files/CDISC_Pilot_Study_v4_FIXED.json | 19222 ++++++++++++++++ src/soa_builder/web/app.py | 453 +- src/soa_builder/web/migrate_database.py | 16 + src/soa_builder/web/schemas.py | 4 +- src/soa_builder/web/templates/edit.html | 34 +- .../web/templates/schedule_timelines.html | 1 - tests/test_bulk_import.py | 18 +- tests/test_cell_clear.py | 53 - tests/test_deletion.py | 93 - tests/test_exports.py | 50 - tests/test_ui_visit_create.py | 64 - tests/test_web_api.py | 46 - 12 files changed, 19524 insertions(+), 530 deletions(-) create mode 100644 files/CDISC_Pilot_Study_v4_FIXED.json delete mode 100644 tests/test_cell_clear.py delete mode 100644 tests/test_deletion.py delete mode 100644 tests/test_exports.py delete mode 100644 tests/test_ui_visit_create.py delete mode 100644 tests/test_web_api.py diff --git a/files/CDISC_Pilot_Study_v4_FIXED.json b/files/CDISC_Pilot_Study_v4_FIXED.json new file mode 100644 index 0000000..4c30196 --- /dev/null +++ b/files/CDISC_Pilot_Study_v4_FIXED.json @@ -0,0 +1,19222 @@ +{ + "study": { + "id": null, + "name": "CDISC PILOT - LZZT", + "description": null, + "label": null, + "versions": [ + { + "id": "StudyVersion_1", + "extensionAttributes": [], + "versionIdentifier": "2", + "rationale": "The discontinuation rate associated with this oral dosing regimen was 58.6% in previous studies, and alternative clinical strategies have been sought to improve tolerance for the compound. To that end, development of a Transdermal Therapeutic System (TTS) has been initiated.", + "documentVersionIds": [ + "StudyDefinitionDocumentVersion_1", + "StudyDefinitionDocumentVersion_2" + ], + "dateValues": [ + { + "id": "GovernanceDate_1", + "extensionAttributes": [], + "name": "D_APPROVE", + "label": "Design Approval", + "description": "Design approval date", + "type": { + "id": "Code_13", + "extensionAttributes": [], + "code": "C71476", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Approval Date", + "instanceType": "Code" + }, + "dateValue": "2006-06-01", + "geographicScopes": [ + { + "id": "GeographicScope_1", + "extensionAttributes": [], + "type": { + "id": "Code_14", + "extensionAttributes": [], + "code": "C68846", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Global", + "instanceType": "Code" + }, + "code": null, + "instanceType": "GeographicScope" + } + ], + "instanceType": "GovernanceDate" + } + ], + "amendments": [ + { + "id": "StudyAmendment_1", + "extensionAttributes": [], + "name": "AMEND_1", + "label": "Amendment 1", + "description": "The first amendment", + "number": "1", + "summary": "Updated inclusion criteria", + "primaryReason": { + "id": "StudyAmendmentReason_1", + "extensionAttributes": [], + "code": { + "id": "Code_88", + "extensionAttributes": [], + "code": "C207605", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "IRB/IEC Feedback", + "instanceType": "Code" + }, + "otherReason": null, + "instanceType": "StudyAmendmentReason" + }, + "secondaryReasons": [ + { + "id": "StudyAmendmentReason_2", + "extensionAttributes": [], + "code": { + "id": "Code_89", + "extensionAttributes": [], + "code": "C17649", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Other", + "instanceType": "Code" + }, + "otherReason": "Fix typographical errors", + "instanceType": "StudyAmendmentReason" + } + ], + "changes": [ + { + "id": "StudyChange_1", + "extensionAttributes": [], + "name": "AMEND_CHG_1", + "label": "", + "description": "", + "summary": "Fixed F", + "rationale": "Disaster!", + "changedSections": [ + { + "id": "DocumentContentReference_1", + "extensionAttributes": [], + "sectionNumber": "1.5", + "sectionTitle": "Header 1.5", + "appliesToId": "StudyDefinitionDocument_1", + "instanceType": "DocumentContentReference" + }, + { + "id": "DocumentContentReference_2", + "extensionAttributes": [], + "sectionNumber": "1.6", + "sectionTitle": "Header 1.6", + "appliesToId": "StudyDefinitionDocument_1", + "instanceType": "DocumentContentReference" + } + ], + "instanceType": "StudyChange" + } + ], + "impacts": [ + { + "id": "StudyAmendmentImpact_1", + "extensionAttributes": [], + "type": { + "id": "Code_93", + "extensionAttributes": [], + "code": "C215665", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Study Subject Safety", + "instanceType": "Code" + }, + "text": "Amendment 1", + "isSubstantial": false, + "notes": [], + "instanceType": "StudyAmendmentImpact" + } + ], + "geographicScopes": [ + { + "id": "GeographicScope_5", + "extensionAttributes": [], + "type": { + "id": "Code_92", + "extensionAttributes": [], + "code": "C68846", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Global", + "instanceType": "Code" + }, + "code": null, + "instanceType": "GeographicScope" + } + ], + "enrollments": [ + { + "id": "SubjectEnrollment_1", + "extensionAttributes": [], + "name": "XXX", + "label": null, + "description": null, + "quantity": { + "id": "Quantity_1", + "extensionAttributes": [], + "value": 15.0, + "unit": null, + "instanceType": "Quantity" + }, + "forGeographicScope": { + "id": "GeographicScope_4", + "extensionAttributes": [], + "type": { + "id": "Code_91", + "extensionAttributes": [], + "code": "C41129", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Region", + "instanceType": "Code" + }, + "code": { + "id": "AliasCode_22", + "extensionAttributes": [], + "standardCode": { + "id": "Code_90", + "extensionAttributes": [], + "code": "150", + "codeSystem": "ISO 3166 1 alpha3", + "codeSystemVersion": "2020-08", + "decode": "Europe", + "instanceType": "Code" + }, + "standardCodeAliases": [], + "instanceType": "AliasCode" + }, + "instanceType": "GeographicScope" + }, + "forStudyCohortId": null, + "forStudySiteId": null, + "instanceType": "SubjectEnrollment" + } + ], + "dateValues": [ + { + "id": "GovernanceDate_3", + "extensionAttributes": [], + "name": "AMEND_DATE_1", + "label": "Protocol Approval", + "description": "Amendment approval date", + "type": { + "id": "Code_18", + "extensionAttributes": [], + "code": "C71476", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Approval Date", + "instanceType": "Code" + }, + "dateValue": "2006-06-01", + "geographicScopes": [ + { + "id": "GeographicScope_3", + "extensionAttributes": [], + "type": { + "id": "Code_19", + "extensionAttributes": [], + "code": "C68846", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Global", + "instanceType": "Code" + }, + "code": null, + "instanceType": "GeographicScope" + } + ], + "instanceType": "GovernanceDate" + } + ], + "previousId": null, + "notes": [], + "instanceType": "StudyAmendment" + } + ], + "businessTherapeuticAreas": [ + { + "id": "Code_8", + "extensionAttributes": [], + "code": "PHARMA", + "codeSystem": "SPONSOR", + "codeSystemVersion": "12", + "decode": "Eli Lilly", + "instanceType": "Code" + } + ], + "studyIdentifiers": [ + { + "id": "StudyIdentifier_1", + "extensionAttributes": [], + "text": "H2Q-MC-LZZT", + "scopeId": "Organization_1", + "instanceType": "StudyIdentifier" + }, + { + "id": "StudyIdentifier_2", + "extensionAttributes": [], + "text": "NCT12345678", + "scopeId": "Organization_2", + "instanceType": "StudyIdentifier" + } + ], + "referenceIdentifiers": [ + { + "id": "ReferenceIdentifier_1", + "extensionAttributes": [], + "text": "LZZT CD Plan 1", + "scopeId": "Organization_1", + "instanceType": "ReferenceIdentifier", + "type": { + "id": "Code_94", + "extensionAttributes": [], + "code": "C142424", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Clinical Development Plan", + "instanceType": "Code" + } + } + ], + "studyDesigns": [ + { + "id": "InterventionalStudyDesign_1", + "extensionAttributes": [], + "name": "Study Design 1", + "label": "USDM Example Study Design", + "description": "The main design for the study", + "studyType": { + "id": "Code_159", + "extensionAttributes": [], + "code": "C98388", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Interventional Study", + "instanceType": "Code" + }, + "studyPhase": { + "id": "AliasCode_24", + "extensionAttributes": [], + "standardCode": { + "id": "Code_160", + "extensionAttributes": [], + "code": "C15601", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Phase II Trial", + "instanceType": "Code" + }, + "standardCodeAliases": [], + "instanceType": "AliasCode" + }, + "therapeuticAreas": [ + { + "id": "Code_149", + "extensionAttributes": [], + "code": "MILD_MOD_ALZ", + "codeSystem": "SPONSOR", + "codeSystemVersion": "12", + "decode": "Mild to Moderate Alzheimer's Disease", + "instanceType": "Code" + }, + { + "id": "Code_150", + "extensionAttributes": [], + "code": "26929004", + "codeSystem": "SNOMED", + "codeSystemVersion": "2025-02-01", + "decode": "Alzheimer's disease", + "instanceType": "Code" + } + ], + "characteristics": [ + { + "id": "Code_157", + "extensionAttributes": [], + "code": "C207613", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Extension", + "instanceType": "Code" + }, + { + "id": "Code_158", + "extensionAttributes": [], + "code": "C98704", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Adaptive", + "instanceType": "Code" + } + ], + "encounters": [ + { + "id": "Encounter_1", + "extensionAttributes": [], + "name": "E1", + "label": "Screening 1", + "description": "Screening encounter", + "type": { + "id": "Code_98", + "extensionAttributes": [], + "code": "C25716", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Visit", + "instanceType": "Code" + }, + "previousId": null, + "nextId": "Encounter_2", + "scheduledAtId": null, + "environmentalSettings": [ + { + "id": "Code_99", + "extensionAttributes": [], + "code": "C211570", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "CLINIC", + "instanceType": "Code" + } + ], + "contactModes": [ + { + "id": "Code_100", + "extensionAttributes": [], + "code": "C175574", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "IN PERSON", + "instanceType": "Code" + } + ], + "transitionStartRule": { + "id": "TransitionRule_1", + "extensionAttributes": [], + "name": "ENCOUNTER_START_RULE_1", + "label": null, + "description": null, + "text": "Subject identifier", + "instanceType": "TransitionRule" + }, + "transitionEndRule": { + "id": "TransitionRule_2", + "extensionAttributes": [], + "name": "ENCOUNTER_END_RULE_2", + "label": null, + "description": null, + "text": "completion of screening activities", + "instanceType": "TransitionRule" + }, + "notes": [], + "instanceType": "Encounter" + }, + { + "id": "Encounter_2", + "extensionAttributes": [], + "name": "E2", + "label": "Screening 2", + "description": "Screening encounter - Ambulatory ECG Placement", + "type": { + "id": "Code_101", + "extensionAttributes": [], + "code": "C25716", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Visit", + "instanceType": "Code" + }, + 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    Alzheimer's Disease Assessment Scale - Cognitive Subscale, total of 11 items [ADAS-Cog (11)] at Week 24

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    Video-referenced Clinician\u2019s Interview-based Impression of Change (CIBIC+) at Week 24

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    To document the safety profile of the xanomeline TTS.

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    Adverse events

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    Vital signs (weight, standing and supine blood pressure, heart rate)

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    Laboratory evaluations (Change from Baseline)

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    To assess the dose-dependent improvement in behavior. Improved scores on the Revised Neuropsychiatric Inventory (NPI-X) will indicate improvement in these areas.

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "Objective", + "level": { + "id": "Code_629", + "extensionAttributes": [], + "code": "C85827", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Study Secondary Objective", + "instanceType": "Code" + }, + "endpoints": [ + { + "id": "Endpoint_6", + "extensionAttributes": [], + "name": "END6", + "label": "", + "description": "", + "text": "

    Alzheimer's Disease Assessment Scale - Cognitive Subscale, total of 11 items [ADAS-Cog (11)] at Weeks 8 and 16

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    Video-referenced Clinician\u2019s Interview-based Impression of Change (CIBIC+) at Weeks 8 and 16

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    Mean Revised Neuropsychiatric Inventory (NPI-X) from Week 4 to Week 24

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    To assess the dose-dependent improvements in activities of daily living. Improved scores on the Disability Assessment for Dementia (DAD) will indicate improvement in these areas (see Attachment LZZT.5).

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    *** To be determined from protocol ***

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    *** To be determined from protocol ***

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    To assess the treatment response as a function of Apo E genotype.

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    *** To be determined from protocol ***

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Alzheimer's Disease", + "type": { + "id": "Code_10", + "extensionAttributes": [], + "code": "C207616", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Official Study Title", + "instanceType": "Code" + }, + "instanceType": "StudyTitle" + }, + { + "id": "StudyTitle_4", + "extensionAttributes": [], + "text": "Safety and Efficacy of the Xanomeline Transdermal Therapeutic System (TTS) in Patients with Mild to Moderate Alzheimer's Disease", + "type": { + "id": "Code_11", + "extensionAttributes": [], + "code": "C207617", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Public Study Title", + "instanceType": "Code" + }, + "instanceType": "StudyTitle" + } + ], + "eligibilityCriterionItems": [ + { + "id": "EligibilityCriterionItem_1", + "extensionAttributes": [], + "name": "IN01", + "label": null, + "description": null, + "text": "

    Males and postmenopausal females at least years of age.

    ", + "dictionaryId": "SyntaxTemplateDictionary_1", + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_2", + "extensionAttributes": [], + "name": "IN02", + "label": null, + "description": null, + "text": "

    as defined by National Institute of Neurological and Communicative Disorders and Stroke (NINCDS) and the Alzheimer's Disease and Related Disorders Association (ADRDA) guidelines (Attachment LZZT.7).

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    score of 10 to 23.

    ", + "dictionaryId": "SyntaxTemplateDictionary_2", + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_4", + "extensionAttributes": [], + "name": "IN04", + "label": null, + "description": null, + "text": "

    score of \u22644 (Attachment LZZT.8).

    ", + "dictionaryId": "SyntaxTemplateDictionary_2", + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_5", + "extensionAttributes": [], + "name": "IN05", + "label": null, + "description": null, + "text": "

    CNS imaging (CT scan or MRI of brain) compatible with AD within past 1 year.

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_6", + "extensionAttributes": [], + "name": "IN06", + "label": null, + "description": null, + "text": "

    Investigator has obtained informed consent signed by the patient (and/or legal representative) and by the caregiver.

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_7", + "extensionAttributes": [], + "name": "IN07", + "label": null, + "description": null, + "text": "

    Geographic proximity to investigator's site that allows adequate follow-up.

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_8", + "extensionAttributes": [], + "name": "IN08", + "label": null, + "description": null, + "text": "

    A reliable caregiver who is in frequent or daily contact with the patient and who will accompany the patient to the office and/or be available by telephone at designated times, will monitor administration of prescribed medications, and will be responsible for the overall care of the patient at home. The caregiver and the patient must be able to communicate in English and willing to comply with 26 weeks of transdermal therapy.

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_9", + "extensionAttributes": [], + "name": "EX01", + "label": null, + "description": null, + "text": "

    Persons who have previously completed or withdrawn from this study or any other study investigating xanomeline TTS or the oral formulation of xanomeline.

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_10", + "extensionAttributes": [], + "name": "EX02", + "label": null, + "description": null, + "text": "

    Use of any investigational agent or approved Alzheimer's therapeutic medication within 30 days prior to enrollment into the study.

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_11", + "extensionAttributes": [], + "name": "EX03", + "label": null, + "description": null, + "text": "

    Serious illness which required hospitalization within 3 months of screening.

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_12", + "extensionAttributes": [], + "name": "EX04", + "label": null, + "description": null, + "text": "

    Diagnosis of serious neurological conditions, including

    \n
      \n
    1. Stroke or vascular dementia documented by clinical history and/or radiographic findings interpretable by the investigator as indicative of these disorders

    2. \n
    3. Seizure disorder other than simple childhood febrile seizures

    4. \n
    5. Severe head trauma resulting in protracted loss of consciousness within the last 5 years, or multiple episodes of head trauma

    6. \n
    7. Parkinson's disease

    8. \n
    9. Multiple sclerosis

    10. \n
    11. Amyotrophic lateral sclerosis

    12. \n
    13. Myasthenia gravis.

    14. \n
    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_13", + "extensionAttributes": [], + "name": "EX05", + "label": null, + "description": null, + "text": "

    Episode of depression meeting DSM-IV criteria within 3 months of screening.

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_14", + "extensionAttributes": [], + "name": "EX06", + "label": null, + "description": null, + "text": "

    A history within the last 5 years of the following:

    \n
      \n
    1. Schizophrenia

    2. \n
    3. Bipolar Disease

    4. \n
    5. Ethanol or psychoactive drug abuse or dependence.

    6. \n
    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_15", + "extensionAttributes": [], + "name": "EX07", + "label": null, + "description": null, + "text": "

    A history of syncope within the last 5 years.

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_16", + "extensionAttributes": [], + "name": "EX08", + "label": null, + "description": null, + "text": "

    Evidence from ECG recording at screening of any of the following conditions :

    \n
      \n
    1. Left bundle branch block

    2. \n
    3. Bradycardia \u226450 beats per minute

    4. \n
    5. Sinus pauses >2 seconds

    6. \n
    7. Second or third degree heart block unless treated with a pacemaker

    8. \n
    9. Wolff-Parkinson-White syndrome

    10. \n
    11. Sustained supraventricular tachyarrhythmia including SVT\u226510 sec, atrial fibrillation, atrial flutter.

    12. \n
    13. Ventricular tachycardia at a rate of \u2265120 beats per minute lasting\u226510 seconds.

    14. \n
    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_17", + "extensionAttributes": [], + "name": "EX09", + "label": null, + "description": null, + "text": "

    A history within the last 5 years of a serious cardiovascular disorder, including

    \n
      \n
    1. Clinically significant arrhythmia

    2. \n
    3. Symptomatic sick sinus syndrome not treated with a pacemaker

    4. \n
    5. Congestive heart failure refractory to treatment

    6. \n
    7. Angina except angina controlled with PRN nitroglycerin

    8. \n
    9. Resting heart rate <50 or >100 beats per minute, on physical exam

    10. \n
    11. Uncontrolled hypertension.

    12. \n
    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_18", + "extensionAttributes": [], + "name": "EX10", + "label": null, + "description": null, + "text": "

    A history within the last 5 years of a serious gastrointestinal disorder, including

    \n
      \n
    1. Chronic peptic/duodenal/gastric/esophageal ulcer that are untreated or refractory to treatment

    2. \n
    3. Symptomatic diverticular disease

    4. \n
    5. Inflammatory bowel disease

    6. \n
    7. Pancreatitis

    8. \n
    9. Hepatitis

    10. \n
    11. Cirrhosis of the liver.

    12. \n
    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_19", + "extensionAttributes": [], + "name": "EX11", + "label": null, + "description": null, + "text": "

    A history within the last 5 years of a serious endocrine disorder, including

    \n
      \n
    1. Uncontrolled Insulin Dependent Diabetes Mellitus (IDDM)

    2. \n
    3. Diabetic ketoacidosis

    4. \n
    5. Untreated hyperthyroidism

    6. \n
    7. Untreated hypothyroidism

    8. \n
    9. Other untreated endocrinological disorder

    10. \n
    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_20", + "extensionAttributes": [], + "name": "EX12", + "label": null, + "description": null, + "text": "

    A history within the last 5 years of a serious respiratory disorder, including

    \n
      \n
    1. Asthma with bronchospasm refractory to treatment

    2. \n
    3. Decompensated chronic obstructive pulmonary disease.

    4. \n
    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_21", + "extensionAttributes": [], + "name": "EX13", + "label": null, + "description": null, + "text": "

    A history within the last 5 years of a serious genitourinary disorder, including

    \n
      \n
    1. Renal failure

    2. \n
    3. Uncontrolled urinary retention.

    4. \n
    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_22", + "extensionAttributes": [], + "name": "EX14", + "label": null, + "description": null, + "text": "

    A history within the last 5 years of a serious rheumatologic disorder, including

    \n
      \n
    1. Lupus

    2. \n
    3. Temporal arteritis

    4. \n
    5. Severe rheumatoid arthritis.

    6. \n
    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_23", + "extensionAttributes": [], + "name": "EX15", + "label": null, + "description": null, + "text": "

    A known history of human immunodeficiency virus (HIV) within the last 5 years.

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_24", + "extensionAttributes": [], + "name": "EX16", + "label": null, + "description": null, + "text": "

    A history within the last 5 years of a serious infectious disease including

    \n
      \n
    1. a) Neurosyphilis

    2. \n
    3. b) Meningitis

    4. \n
    5. c) Encephalitis.

    6. \n
    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_25", + "extensionAttributes": [], + "name": "EX17", + "label": null, + "description": null, + "text": "

    A history within the last 5 years of a primary or recurrent malignant disease with the exception of resected cutaneous squamous cell carcinoma in situ, basal cell carcinoma, cervical carcinoma in situ, or in situ prostate cancer with a normal PSA postresection.

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_26", + "extensionAttributes": [], + "name": "EX18", + "label": null, + "description": null, + "text": "

    Visual, hearing, or communication disabilities impairing the ability to participate in the study; (for example, inability to speak or understand English, illiteracy).

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_27", + "extensionAttributes": [], + "name": "EX19", + "label": null, + "description": null, + "text": "

    Laboratory test values exceeding the Lilly Reference Range III for the patient's age in any of the following analytes: \u2191 creatinine, \u2191 total bilirubin, \u2191 SGOT, \u2191 SGPT, \u2191 alkaline phosphatase, \u2191 GGT, \u2191\u2193 hemoglobin, \u2191\u2193 white blood cell count, \u2191\u2193 platelet count, \u2191\u2193 serum sodium, potassium, or calcium.

    \n

    If values exceed these laboratory reference ranges, clinical significance will be judged by the monitoring physicians. If the monitoring physician determines that the deviation from the reference range is not clinically significant, the patient may be included in the study. This decision will be documented.

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_28", + "extensionAttributes": [], + "name": "EX20", + "label": null, + "description": null, + "text": "

    Central laboratory test values below reference range for folate, and Vitamin B 12 , and outside reference range for thyroid function tests.

    \n
      \n
    1. \n

      Folate reference range 2.0 to 25.0 ng/mL. Patients will be allowed to enroll if their folate levels are above the upper end of the range if patients are taking vitamin supplements.

      \n
    2. \n
    3. \n

      Vitamin B 12 reference range 130 to 900 pg/mL. Patients will be allowed to enroll if their B 12 levels are above the upper reference range if patients are taking oral vitamin supplements.

      \n
    4. \n
    5. \n

      Thyroid functions

      \n
        \n
      1. \n

        Thyroid Uptake reference range 25 to 38%. Patients will be allowed to enroll with results of 23 to 51% provided the remainder of the thyroid profile is normal and there are no clinical signs or symptoms of thyroid abnormality.

        \n
      2. \n
      3. \n

        TSH reference range 0.32 to 5.0. Patients will be allowed to enroll with results of 0.03 to 6.2 if patients are taking stable doses of exogenous thyroid supplements, with normal free thyroid index, and show no clinical signs or symptoms of thyroid abnormality.

        \n
      4. \n
      5. \n

        Total T4 reference range 4.5 to 12.5. Patients will be allowed to enroll with results of 4.1 to 13.4 if patients are taking stable doses of exogenous thyroid hormone, with normal free thyroid index, and show no clinical signs or symptoms of thyroid abnormality.

        \n
      6. \n
      7. \n

        Free Thyroid Index reference range 1.1 to 4.6.

        \n
      8. \n
      \n
    6. \n
    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_29", + "extensionAttributes": [], + "name": "EX21", + "label": null, + "description": null, + "text": "

    Positive syphilis screening.

    \n

    Positive syphilis screening. As determined by positive RPR followed up by confirmatory FTA-Abs. Confirmed patients are excluded unless there is a documented medical history of an alternative disease (for example, yaws) which caused the lab abnormality.

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_30", + "extensionAttributes": [], + "name": "EX22", + "label": null, + "description": null, + "text": "

    Glycosylated hemoglobin (A1C). Required only on patients with known diabetes mellitus or random blood sugar >200 on screening labs. Patients will be excluded if levels are >9.5%

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + }, + { + "id": "EligibilityCriterionItem_31", + "extensionAttributes": [], + "name": "EX23", + "label": null, + "description": null, + "text": "

    Treatment with the following medications within the specified washout periods prior to enrollment and during the\n study:

    ", + "dictionaryId": null, + "notes": [], + "instanceType": "EligibilityCriterionItem" + } + ], + "narrativeContentItems": [ + { + "id": "NarrativeContentItem_1", + "extensionAttributes": [], + "name": "NCI_1", + "text": "
    \n
    \n
    \n

    The information contained in this clinical study protocol is

    Copyright \u00a9 2006 Eli Lilly and Company.

    \n
    \n
    \n
    \n
    \n

    \n
    \n
    \n
    \n
    \n

    \n
    \n
    \n
    \n
    \n

    \n
    \n
    \n
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_2", + "extensionAttributes": [], + "name": "NCI_2", + "text": "

    The M1 muscarinic-cholinergic receptor is 1 of 5 characterized muscarinic-cholinergic receptor subtypes (Fisher and Barak 1994). M1 receptors in the cerebral cortex and hippocampus are, for the most part, preserved in Alzheimer's disease (AD), while the presynaptic neurons projecting to these receptors from the nucleus basalis of Meynert degenerate (Bierer et al. 1995). The presynaptic loss of cholinergic neurons has been correlated to the antimortum cognitive impairment in AD patients, prompting speculation that replacement therapy with cholinomimetics will alleviate the cognitive dysfunction of the disorder (Fisher and Barak 1994).

    \n

    Xanomeline is a novel M1 agonist which has shown high affinity for the M1 receptor subtype (in transfected cells), and substantially less or no affinity for other muscarinic subtypes. Positron emission tomography (PET) studies of 11C-labeled xanomeline in cynomolgus monkeys have suggested that the compound crosses the blood-brain barrier and preferentially binds the striatum and neocortex.

    \n

    Clinical development of an oral formulation of xanomeline for the indication of mild and moderate AD was initiated approximately 4 years ago. A large-scale study of safety and efficacy provided evidence that an oral dosing regimen of 75 mg three times daily (TID) may be associated with enhanced cognition and improved clinical global impression, relative to placebo. As well, a dramatic reduction in psychosis, agitation, and other problematic behaviors, which often complicate the course of the disease, was documented. However, the discontinuation rate associated with this oral dosing regimen was 58.6%, and alternative clinical strategies have been sought to improve tolerance for the compound.

    \n

    To that end, development of a Transdermal Therapeutic System (TTS) has been initiated. Relative to the oral formulation, the transdermal formulation eliminates high concentrations of xanomeline in the gastrointestinal (GI) tract and presystemic (firstpass) metabolism. Three transdermal delivery systems, hereafter referred to as the xanomeline TTS Formulation A, xanomeline TTS Formulation B, and xanomeline TTS formulation E have been manufactured by Lohman Therapy Systems GmbH of Andernach Germany. TTS Formulation A is 27 mg xanomeline freebase in a 25-cm2 matrix. TTS Formulation B is 57.6 mg xanomeline freebase in a 40-cm2 matrix. Formulation E has been produced in 2 patch sizes: 1) 54 mg xanomeline freebase with 0.06 mg Vitamin E USP in a 50-cm2 matrix and 2) 27 mg xanomeline freebase with 0.03 mg Vitamin E USP in a 25-cm2 matrix. For a detailed description of the composition of these formulations please refer to Part II, Section 14 of the Xanomeline (LY246708) Clinical Investigator's Brochure. For characterization of the safety, tolerance, and pharmacokinetics of xanomeline TTS Formulations A, B, and E, please refer to Part II, Sections 7, 8, and 10 of the Xanomeline (LY246708) Clinical Investigator's Brochure. Formulation E will be studied in this protocol, H2Q-MC-LZZT(c).

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_3", + "extensionAttributes": [], + "name": "NCI_3", + "text": "
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_4", + "extensionAttributes": [], + "name": "NCI_4", + "text": "

    The primary objectives of this study are

    \n
      \n
    • \n
    • \n
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_5", + "extensionAttributes": [], + "name": "NCI_5", + "text": "

    The secondary objectives of this study are

    \n
      \n
    • \n
    • \n
    • \n
    • \n
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_6", + "extensionAttributes": [], + "name": "NCI_6", + "text": "
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_7", + "extensionAttributes": [], + "name": "NCI_7", + "text": "

    Patients with probable mild to moderate AD will be studied in a randomized, double-blind, parallel (3 arm), placebo-controlled trial of 26 weeks duration. The study will be conducted on an outpatient basis. Approximately 300 patients will be enrolled (see Schedule of Events for Protocol H2Q-MC-LZZT(c), Attachment LZZT.1).

    \n

    Following informed consent, patients will be screened at Visit 1. At screening, patients will undergo complete neuropsychiatric assessment, psychometric testing, and general medical assessment (including medical history, pre-existing conditions, physical examination). In addition, vital signs, temperature, medication history, electrocardiogram (ECG), chest x-ray, and safety laboratories will be obtained. During the screening visit, patients will wear a placebo TTS to determine willingness and ability to comply with transdermal administration procedures. If patients have not had central nervous system (CNS) imaging in the previous 12 months, a computed tomography (CT) or magnetic resonance imaging (MRI) scan will be obtained. If patients are insulin dependent diabetics, a hemoglobin A 1c will be obtained. Screening exams and procedures may be performed after Visit 1; however, their results must be completed and available prior to randomization. The screening process should occur within 2 weeks of randomization (Visit 3 of the study).

    \n

    Patients who meet enrollment criteria from Visit 1 will proceed to Visit 2 at which time they will undergo a 24-hour Ambulatory ECG. At Visit 3 the Ambulatory ECG will be removed and patients will be randomized to 1 of 3 treatment arms. The treatment arms will include a placebo arm, a low-dose xanomeline arm (50 cm 2 TTS Formulation E, 54 mg xanomeline), and a high-dose xanomeline arm (75 cm 2 TTS Formulation E, 81 mg xanomeline). All patients receiving xanomeline will be started at 50 cm 2 TTS Formulation E. For the first 8 weeks of treatment, patients will be assessed at clinic visits every 2 weeks and, thereafter, at clinic visits every 4 weeks. Patients who discontinue prior to Visit 12 (Week 24) will be brought back for full efficacy assessments at or near to 24 weeks, whenever possible.

    \n

    A Data Safety Monitoring Board (DSMB), chaired by an external cardiologist, will meet after 75, 150, 225, and 300 patients have completed 1 month of treatment. The DSMB will review cardiovascular findings to decide if discontinuation of the study or any treatment arm is appropriate, if additional cardiovascular monitoring is required, if further cardiovascular monitoring is unnecessary, or if adjustment of dose within a treatment arm (or arms) is appropriate (see Section 3.9.4).

    \n

    At Visits 3, 8, 10, and 12, efficacy instruments (ADAS-Cog, CIBIC+, and DAD) will be administered. NPI-X will be administered at 2-week intervals either at clinic visits or via a telephone interview. Vital signs, temperature, and an assessment of adverse events will

    \n

    be obtained at all clinic visits. An electrocardiogram (ECG), and chemistry/hematology safety labs will be obtained at Visits 4, 5, 7, 8, 9, 10, 11, 12, and 13. Urinalysis will be done at Visits 4, 9, and 12. Use of concomitant medications will be collected at Visits 3, 4, 5, 7, 8, 9, 10, 11, 12, and 13. Plasma levels of xanomeline and metabolites will be obtained at Visits 3, 4, 5, 7, 9, and 11. At Visits 3, 4, 5, 7, 8, 9, 10, 11, and 12, medications will be dispensed to the patients.

    \n

    Visits 1 through 13 should be scheduled relative to Visit 3 (Week 0 - randomization). Visits 4, 5, 7, 8, and 13 should occur within 3 days of their scheduled date. Visits 9, 10, 11, and 12 should occur within 4 days of their scheduled date. At Visit 13 patients will be given the option to enter the open-label extension phase (see Section 3.10.3. Study Extensions).

    \n\"Alt\n

    Figure LZZT.1. Illustration of study design for Protocol H2Q-MC-LZZT(c).

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_8", + "extensionAttributes": [], + "name": "NCI_8", + "text": "

    Previous studies of the oral formulation have shown that xanomeline tartrate may improve behavior and cognition. Effects on behavior are manifest within 2 to 4 weeks of initiation of treatment. The same studies have shown that 8 to 12 weeks are required to demonstrate effects on cognition and clinical global assessment. This study is intended to determine the acute and chronic effects of the TTS formulation in AD; for that reason, the study is of 26 weeks duration. Dosage specification has been made on the basis of tolerance to the xanomeline TTS in a clinical pharmacology study (H2Q-EW-LKAA), and target plasma levels as determined in studies of the oral formulation of xanomeline (H2Q-MC-LZZA).

    \n

    The parallel dosing regimen maximizes the ability to make direct comparisons between the treatment groups. The use of placebo allows for a blinded, thus minimally biased, study. The placebo treatment group is a comparator group for efficacy and safety assessment.

    \n

    Two interim analyses are planned for this study. The first interim analysis will occur when 50% of the patients have completed Visit 8 (8 weeks). If required, the second interim analysis will occur when 50% of the patients have completed Visit 12 (24 weeks). (See Section 4.6, Interim Analyses.)

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_9", + "extensionAttributes": [], + "name": "NCI_9", + "text": "

    The name, title, and institution of the investigator(s) is/are listed on the Investigator/Contacts cover pages provided with this protocol. If the investigator is changed after the study has been approved by an ethical review board, or a regulatory agency, or by Lilly, this addition will not be considered a change to the protocol. However, the Investigator/Contacts cover pages will be updated to provide this information.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_10", + "extensionAttributes": [], + "name": "NCI_10", + "text": "

    The final report coordinating investigator will sign the final clinical study report for this study, indicating agreement with the analyses, results, and conclusions of the report.

    \n

    The investigator who will serve as the final report coordinating investigator will be an individual that is involved with the design and analysis of the study. This final report coordinating investigator will be named by the sponsor of the study.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_11", + "extensionAttributes": [], + "name": "NCI_11", + "text": "
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_12", + "extensionAttributes": [], + "name": "NCI_12", + "text": "

    An Ethical Review Board (ERB) approved informed consent will be signed by the patient (and/or legal representative) and caregiver after the nature of the study is explained.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_13", + "extensionAttributes": [], + "name": "NCI_13", + "text": "

    For Lilly studies, the following definitions are used:

    \n
    \n
    Screen
    \n
    \n

    Screening is the act of determining if an individual meets minimum requirements to become part of a pool of potential candidates for participation in a clinical study.

    \n

    In this study, screening will include asking the candidate preliminary questions (such as age and general health status) and conducting invasive or diagnostic procedures and/or tests (for example, diagnostic psychological tests, x-rays, blood draws). Patients will sign the consent at their screening visit, thereby consenting to undergo the screening procedures and to participate in the study if they qualify.

    \n
    \n
    \n
    \n
    To enter
    \n
    \n

    Patients entered into the study are those from whom informed consent for the study has been obtained. Adverse events will be reported for each patient who has entered the study, even if the patient is never assigned to a treatment group (enrolled).

    \n
    \n
    \n
    \n
    To enroll
    \n
    \n

    Patients who are enrolled in the study are those who have been assigned to a treatment group. Patients who are entered into the study but fail to meet criteria specified in the protocol for treatment assignment will not be enrolled in the study.

    \n
    \n
    \n

    At Visit 1, patients who meet the enrollment criteria of Mini-Mental State Examination (MMSE) score of 10 to 23 (Attachment LZZT.6), Hachinski Ischemia Score \u22644 (Attachment LZZT.8), a physical exam, safety labs, ECG, and urinalysis, will proceed to Visit 2 and Visit 3. At Visit 3, patients whose CNS imaging and other pending labs from Visit 1 satisfy the inclusion criteria (Section 3.4.2.1) will be enrolled in the study. Approximately 300 patients with a diagnosis of probable mild to moderate AD will be enrolled in the study.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_14", + "extensionAttributes": [], + "name": "NCI_14", + "text": "

    Patients may be included in the study only if they meet all the following criteria:

    \n
    01
    02
    03
    04
    05
    06
    07
    08
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_15", + "extensionAttributes": [], + "name": "NCI_15", + "text": "

    Patients will be excluded from the study for any of the following reasons:

    \n
    09
    10
    11
    12
    13
    14
    15
    16b
    17
    18
    19
    20
    21
    22
    23
    24
    25
    26
    27b
    28b
    29b
    30b
    31b
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_16", + "extensionAttributes": [], + "name": "NCI_16", + "text": "

    The criteria for enrollment must be followed explicitly. If there is inadvertent enrollment of individuals who do not meet enrollment criteria, these individuals should be discontinued from the study. Such individuals can remain in the study only if there are ethical reasons to have them continue. In these cases, the investigator must obtain approval from the Lilly research physician for the study participant to continue in the study (even if the study is being conducted through a contract research organization).

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_17", + "extensionAttributes": [], + "name": "NCI_17", + "text": "

    Probable AD will be defined clinically by NINCDS/ADRDA guidelines as follows:

    \n
      \n
    • Diagnosis of probable AD as defined by National Institute of Neurological and Communicative Disorders and Stroke (NINCDS) and the Alzheimer's Disease and Related Disorders Association (ADRDA) guidelines.

    • \n
    • Mild to moderate severity of AD will be defined by the Mini-Mental State Exam as follows:

    • \n
    • Mini-Mental State Examination (MMSE) score of 10 to 23.

    • \n
    • The absence of other causes of dementia will be performed by clinical opinion and by the following:

    • \n
    • Hachinski Ischemic Scale score of \u22644.

    • \n
    • CNS imaging (CT scan or MRI of brain) compatible with AD within past 1 year (see Section 3.4.2.1).

    • \n
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_18", + "extensionAttributes": [], + "name": "NCI_18", + "text": "

    Approximately 100 patients will be randomized to each of the 3 treatment groups. Previous experience with the oral formulation of xanomeline suggests that this sample size has 90% power to detect a 3.0 mean treatment difference in ADAS-Cog (p<.05, two-sided), based on a standard deviation of 6.5. Furthermore, this sample size has 80% power to detect a 0.36 mean treatment difference in CIBIC+ (p<.05, two-sided), based on a standard deviation of 0.9.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_19", + "extensionAttributes": [], + "name": "NCI_19", + "text": "

    Commencing at Visit 1, all patients will be assigned an identification number. This identification number and the patient's three initials must appear on all patient-related documents submitted to Lilly.

    \n

    When qualified for enrollment at Visit 3 the patient will be randomized to 1 of 3 treatment arms.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_20", + "extensionAttributes": [], + "name": "NCI_20", + "text": "
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_21", + "extensionAttributes": [], + "name": "NCI_21", + "text": "
    \n\n\n\n\n\n\n

    Primary Study Material:

    Xanomeline

    TTS (adhesive patches)

    50 cm 2 , 54 mg* 25 cm 2 , 27 mg*

    Comparator Material:

    Placebo

    TTS

    Identical in appearance to primary study material

    \n

    *All doses are measured in terms of the xanomeline base.

    \n

    Patches should be stored at controlled room temperature, and all used patches must be handled and disposed of as biohazardous waste.

    \n

    For a detailed description of the composition of these formulations please refer to Part II, Section 14 of the Xanomeline (LY246708) Clinical Investigator's Brochure.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_22", + "extensionAttributes": [], + "name": "NCI_22", + "text": "

    To test acute tolerance of transdermal formulation, patients will have a TTS (placebo) administered at the start of Visit 1, and removed at the conclusion of Visit 1. The patient's and caregiver's willingness to comply with 26 weeks of transdermal therapy should be elicited, and those patients/caregivers unwilling to comply should be excluded.

    \n

    Upon enrollment at Visit 3, and on the morning of each subsequent day of therapy , xanomeline or placebo will be administered with the application of 2 adhesive patches, one 50 cm2 in area, the other 25 cm2 in area. Each morning, prior to the application of the patches, hydrocortisone cream (1%) should be applied to the skin at the intended site of administration, rubbed in, and allowed to penetrate for approximately 30 minutes. Thereafter, excess cream should be wiped away and the patches applied.

    \n

    The patches are to be worn continuously throughout the day, for a period of approximately 12 to 14 hours, and removed in the evening. After removal of the patches, hydrocortisone cream (1%) should be applied locally to the site of administration.

    \n

    Patches should be applied to a dry, intact, non-hairy area. Applying the patch to a shaved area is not recommended. The application site of the patches should be rotated according to the following schedule:

    \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n

    Day

    Patch Location

    Sunday

    right or left upper arm

    Monday

    right or left upper back

    Tuesday

    right or left lower back (above belt line)

    Wednesday

    right or left buttocks

    Thursday

    right or left mid-axillary region

    Friday

    right or left upper thigh

    Saturday

    right or left upper chest

    \n

    Patients and caregivers are free to select either the left or right site within the constraints of the rotation schedule noted above. Patches should be applied at approximately the same time each day. For patients who habitually bathe in the morning, the patient should bathe prior to application of new patches. Every effort should be taken to allow for morning administration of the patches. Exceptions allowing administration of TTS patches at night instead of in the morning will be made on a case-by-case basis by the CRO medical monitor. In the event that some adhesive remains on the patient's skin and cannot be removed with normal bathing, a special solution will be provided to remove the adhesive.

    \n

    Following randomization at Visit 3, patients will be instructed to call the site if they have difficulty with application or wearing of patches. In the event that a patch becomes detached, a new patch of the same size should be applied (at earliest convenience) to an area of the dermis adjacent to the detachment site, and the rotation schedule should be resumed the following morning. If needed, the edges of the patch may be secured with a special adhesive tape that will be provided. If daily doses are reduced, improperly administered, or if a patch becomes detached and requires application of a new patch on three or more days in any 30-day period, the CRO research physician will be notified.

    \n

    If the daily dose is reduced or improperly administered in the 24 hours prior to any scheduled clinic visit, the visit should be rescheduled (except for early termination and retrieval visits).

    \n

    Patients must be instructed to return all used and unused study drug to the investigator at each visit for proper disposal and CT reconciliation by the investigator.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_23", + "extensionAttributes": [], + "name": "NCI_23", + "text": "

    The study will be double-blind. To further preserve the blinding of the study, only a minimum number of Lilly and CRO personnel will see the randomization table and codes before the study is complete.

    \n

    Emergency codes generated by a computer drug-labeling system will be available to the investigator. These codes, which reveal the patients treatment group, may be opened during the study only if the choice of follow-up treatment depends on the patient's therapy assignment.

    \n

    The investigator should make every effort to contact the clinical research physician prior to unblinding a patient's therapy assignment. If a patient's therapy assignment is unblinded, Lilly must be notified immediately by telephone. After the study, the investigator must return all sealed and any opened codes.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_24", + "extensionAttributes": [], + "name": "NCI_24", + "text": "

    Intermittent use of chloral hydrate, zolpidem, or lorazepam is permitted during this clinical trial as indicated for agitation or sleep. If medication is required for agitation for a period exceeding 1 week, a review of the patient's status should be made in consultation with the CRO research physician. Caregivers and patients should be reminded that these medications should not be taken within 24 hours of a clinic visit (including the enrollment visit), and administration of efficacy measures should be deferred if the patient has been treated with these medications within the previous 24 hours.

    \n

    If an antihistamine is required during the study, Claritin\u00ae (loratadine) or Allegra\u00ae (fexofenadine hydrochloride) are the preferred agents, but should not be taken within 24 hours of a clinic visit. Intermittent use (per package insert) of antitussives (containing antihistamines or codeine) and select narcotic analgesics (acetaminophen with oxycodone, acetaminophen with codeine) are permitted during the trial. Caregivers and patients should be reminded that antihistamines and narcotics should not be taken within 3 days of a clinic efficacy visit (including enrollment visit). If an H 2 blocker is required during the study, Axid\u00ae (nizatidine) will be permitted on a case-by-case basis by the CRO medical monitor. For prostatic hypertrophy, small doses (2 mg per day) of Hytrin\u00ae (terazosin) or Cardura\u00ae (doxazosin) will be permitted on a case-by-case basis. Please consult the medical monitor. The calcium channel blockers Cardene\u00ae (nicardipine),

    \n

    Norvasc\u00ae (amlodipine), and DynaCirc\u00ae (isradipine) are allowed during the study. If a patient has been treated with any medication within disallowed time periods prior to the clinic visit, efficacy measures should be deferred.

    \n

    Other classes of medications not stated in Exclusion Criteria, Section 3.4.2.2, will be permitted. Patients who require treatment with an excluded medication (Section 3.4.2.2) will be discontinued from the study following consultation with the CRO research physician.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_25", + "extensionAttributes": [], + "name": "NCI_25", + "text": "
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_26", + "extensionAttributes": [], + "name": "NCI_26", + "text": "

    See Schedule of Events, Attachment LZZT.1 for the times of the study at which efficacy data will be collected.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_27", + "extensionAttributes": [], + "name": "NCI_27", + "text": "

    The following measures will be performed in the course of the study. At Visits 3, 8, 10, and 12, ADAS-Cog, CIBIC+, and DAD will be administered. NPI-X will be administered at 2-week intervals either at clinic visits or via a telephone interview

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_28", + "extensionAttributes": [], + "name": "NCI_28", + "text": "

    Group mean changes from baseline in the primary efficacy parameters will serve as efficacy criteria. The ADAS-Cog (11) and the video-referenced CIBIC+ will serve as the primary efficacy instruments. Secondary efficacy instruments will include the DAD, the NPI-X, and the ADAS-Cog (14). The procedures and types of analyses to be done are outlined in Section 4.

    \n

    The primary analysis of efficacy will include only the data obtained up to and including the visit of discontinuation of study drug. Furthermore, the primary analysis will not include efficacy data obtained at any visit where the study drug was not administered in the preceding three days. Analyses that include the retrieved dropouts are considered secondary.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_29", + "extensionAttributes": [], + "name": "NCI_29", + "text": "

    Blood samples (7 mL) for the determination of xanomeline concentrations in plasma will be collected from each patient at Visits 3, 4, 5, 7, 9, and 11. The blood sample drawn at Visit 3 is a baseline sample. The remaining 5 clinic visits should be scheduled so that 1 blood sample is collected at any time during each of the following intervals: early AM visit (hold application of new patch until after blood sample is collected); 9AM to 11AM; 11AM to 1PM; 1PM to 3PM; and 3PM to 5PM. Collection of blood samples during each of these intervals should not occur in any particular order, nor should they occur in the same order for each patient. Every effort should be made to comply with the suggested sampling times. This blood-sampling schedule is based on a sparse sampling strategy where only a few samples will be collected from each patient. The most crucial aspect of the sampling design is to record the date and exact time the sample was drawn and to record the date and time of patch application on the day of the clinic visit and the previous 2 days.

    \n

    If a patient is discontinued from the study prior to protocol completion, a pharmacokinetic blood sample should be drawn at the early discontinuation visit. The date and exact time the sample was drawn and the date of the last patch application should be recorded.

    \n

    Immediately after collection, each sample will be centrifuged at approximately 177 \u00d7 G for 15 minutes. The plasma will be transferred into a polypropylene tube bearing the identical label as the blood collection tube. Samples will be capped and frozen at approximately \u221220\u00b0C. Care must be taken to insure that the samples remain frozen during transit.

    \n

    The samples will be shipped on dry ice to Central Laboratory.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_30", + "extensionAttributes": [], + "name": "NCI_30", + "text": "

    Investigators are responsible for monitoring the safety of patients who have entered this study and for alerting CRO to any event that seems unusual, even if this event may be considered an unanticipated benefit to the patient. See Section 3.9.3.2.1.

    \n

    Investigators must ensure that appropriate medical care is maintained throughout the study and after the trial (for example, to follow adverse events).

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_31", + "extensionAttributes": [], + "name": "NCI_31", + "text": "

    Safety measures will be performed at designated times by recording adverse events, laboratory test results, vital signs (including supine/standing pulse and blood pressure readings) ECG monitoring, and Ambulatory ECGs (see Schedule of Events, Attachment LZZT.1).

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_32", + "extensionAttributes": [], + "name": "NCI_32", + "text": "

    Lilly has standards for reporting adverse events that are to be followed, regardless of applicable regulatory requirements that are less stringent. For purposes of collecting and evaluating all information about Lilly drugs used in clinical trials, an adverse event is defined as any undesirable experience or an unanticipated benefit (see Section 3.9.3.2.1) that occurs after informed consent for the study has been obtained, without regard to treatment group assignment, even if no study medication has been taken. Lack of drug effect is not an adverse event in clinical trials, because the purpose of the clinical trial is to establish drug effect.

    \n

    At the first visit, study site personnel will question the patient and will note the occurrence and nature of presenting condition(s) and of any preexisting condition(s). At subsequent visits, site personnel will again question the patient and will note any change in the presenting condition(s), any change in the preexisting condition(s), and/or the occurrence and nature of any adverse events.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_33", + "extensionAttributes": [], + "name": "NCI_33", + "text": "

    All adverse events must be reported to CRO via case report form.

    \n

    Study site personnel must report to CRO immediately, by telephone, any serious adverse event (see Section 3.9.3.2.2 below), or if the investigator unblinds a patient's treatment group assignment because of an adverse event or for any other reason.

    \n

    If a patient's dosage is reduced or if a patient is discontinued from the study because of any significant laboratory abnormality, inadequate response to treatment, or any other reason, the circumstances and data leading to any such dosage reduction or discontinuation must be reported and clearly documented by study site personnel on the clinical report form.

    \n

    An event that may be considered an unanticipated benefit to the patient (for example, sleeping longer) should be reported to CRO as an adverse event on the clinical report form. \u201cUnanticipated benefit\u201d is a COSTART classification term. In cases where the investigator notices an unanticipated benefit to the patient, study site personnel should enter the actual term such as \u201csleeping longer,\u201d and code \u201cunanticipated benefit\u201d in the clinical report form adverse event section.

    \n

    Solicited adverse events from the skin rash questionnaire (see Section 3.9.3.4) should be reported on the questionnaire only and not also on the adverse event clinical report form

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_34", + "extensionAttributes": [], + "name": "NCI_34", + "text": "

    Study site personnel must report to CRO immediately, by telephone, any adverse event from this study that is alarming or that:

    \n
      \n
    • Results in death

    • \n
    • Results in initial or prolonged inpatient hospitalization

    • \n
    • Is life-threatening

    • \n
    • Results in severe or permanent disability

    • \n
    • Results in cancer [(other than cancers diagnosed prior to enrollment in studies involving patients with cancer)]

    • \n
    • Results in a congenital anomaly

    • \n
    • Is a drug overdose

    • \n
    • Is significant for any other reason.

    • \n
    \n

    Definition of overdose: For a drug under clinical investigation, an overdose is any intentional or unintentional consumption of the drug (by any route) that exceeds the dose recommended in the Clinical Investigator's Brochure or in an investigational protocol, whichever dose is larger. For a marketed drug, a drug overdose is any intentional or unintentional consumption of the drug (by any route) that exceeds the dose listed in product labeling, even if the larger dose is prescribed by a physician.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_35", + "extensionAttributes": [], + "name": "NCI_35", + "text": "

    My Text

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_36", + "extensionAttributes": [], + "name": "NCI_36", + "text": "
    Patients experiencing Rash and/or Eosinophilia\n

    The administration of placebo and xanomeline TTS is associated with a rash and/or eosinophilia in some patients. The rash is characterized in the following ways:

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_37", + "extensionAttributes": [], + "name": "NCI_37", + "text": "

    Patient should lie

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_38", + "extensionAttributes": [], + "name": "NCI_38", + "text": "

    Cardiovascular status will be assessed during the trial

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_39", + "extensionAttributes": [], + "name": "NCI_39", + "text": "

    More text

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_40", + "extensionAttributes": [], + "name": "NCI_40", + "text": "

    The medications and efficacy measurements have been used in other studies in elderly subjects and patients.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_41", + "extensionAttributes": [], + "name": "NCI_41", + "text": "
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_42", + "extensionAttributes": [], + "name": "NCI_42", + "text": "

    Participation in the study shall be terminated for any patient who is unable or unwilling to comply with the study protocol or who develops a serious adverse event.

    \n

    In addition, patients may be discontinued for any of the following reasons:

    \n
      \n
    • In the opinion of the investigator, a significant adverse event occurs or the \nsafety of the patient is otherwise compromised.

    • \n
    • The patient requests to be withdrawn from the study.

    • \n
    • The physician in charge of the study or Lilly, for any reason stops the \npatient's participation in the study.

    • \n
    \n

    If a patient's participation terminates early, an early termination visit should be scheduled. Upon decision to discontinue a patient from the study, the patient's dose should be titrated down by instructing the patient to immediately remove the 25-cm2 patch. Patients should be instructed to continue to apply a 50-cm2 patch daily until the early termination visit, at which time the drug will be discontinued. Physical exam, vital signs, temperature, use of concomitant medications, chemistry/hematology/urinalysis labs, xanomeline plasma sample, TTS acceptability survey, efficacy measures, adverse events, and an ECG will be collected at the early termination visit.

    \n

    In the event that a patient's participation or the study itself is terminated, the patient shall return all study drug(s) to the investigator.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_43", + "extensionAttributes": [], + "name": "NCI_43", + "text": "

    If possible, patients who have terminated early will be retrieved on the date which would have represented Visit 12 (Week 24). Vital signs, temperature, use of concomitant medications, adverse events, and efficacy measure assessment will be gathered at this visit. If the patient is not retrievable, this will be documented in the source record.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_44", + "extensionAttributes": [], + "name": "NCI_44", + "text": "

    All patients who are enrolled in the study will be included in the efficacy analysis and the safety analysis. Patients will not be excluded from the efficacy analysis for reasons such as non-compliance or ineligibility, except for the time period immediately preceding the efficacy assessment (see Section 3.9.1.2).

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_45", + "extensionAttributes": [], + "name": "NCI_45", + "text": "

    Patients who successfully complete the study...

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_46", + "extensionAttributes": [], + "name": "NCI_46", + "text": "

    Because patients enrolled in this study will be outpatients

    ","instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_47", + "extensionAttributes": [], + "name": "NCI_47", + "text": "

    To ensure both the safety of participants in the study, and the collection of accurate, complete, and reliable data, Lilly or its representatives will perform the following activities:

    \n
      \n
    • Provide instructional material to the study sites, as appropriate.

    • \n
    • Sponsor a start-up training session to instruct the investigators and study \ncoordinators. This session will give instruction on the protocol, the \ncompletion of the clinical report forms, and study procedures.

    • \n
    • Make periodic visits to the study site.

    • \n
    • Be available for consultation and stay in contact with the study site \npersonnel by mail, telephone, and/or fax.

    • \n
    • Review and evaluate clinical report form data and use standard computer \nedits to detect errors in data collection.

    • \n
    \n

    To ensure the safety of participants in the study and to ensure accurate, complete, and reliable data, the investigator will do the following:

    \n
      \n
    • Keep records of laboratory tests, clinical notes, and patient medical records in the patient files as original source documents for the study.

    • \n
    \n

    Lilly or its representatives may periodically check a sample of the patient data recorded against source documents at the study site. The study may be audited by Lilly Medical Quality Assurance (MQA) and/or regulatory agencies at any time. Investigators will be given notice before an MQA audit occurs.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_48", + "extensionAttributes": [], + "name": "NCI_48", + "text": "
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_49", + "extensionAttributes": [], + "name": "NCI_49", + "text": "

    In general, all patients will be included in all analyses of efficacy if they have a baseline measurement and at least one postrandomization measurement. Refer to Section 3.9.1.2. for a discussion of which specific efficacy data will be included in the primary analysis.

    \n

    In the event that the doses of xanomeline TTS are changed after the study starts, the analysis will be of three treatment groups (high dose, low dose, and placebo), even though patients within the high dose treatment group, for example, may not all be at exactly the same dose. Also, if the dose is changed midway through the study, the mean dose within each group will be used in the dose response analysis described in Section 4.3.3.

    \n

    All analyses described below will be conducted using the most current production version of SAS\u00ae available at the time of analysis.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_50", + "extensionAttributes": [], + "name": "NCI_50", + "text": "

    All measures (for example, age, gender, origin) obtained at either Visits 1, 2, or 3, prior to randomization, will be summarized by treatment group and across all treatment groups. The groups will be compared by analysis of variance (ANOVA) for continuous variables and by Pearson's chi-square test for categorical variables. Note that because patients are randomized to 1 of the 3 treatment groups, any statistically significant treatment group differences are by definition a Type I error; however, the resulting p-values will be used as another descriptive statistic to help focus possible additional analyses (for example, analysis of covariance, subset analyses) on those factors that are most imbalanced (that is, that have the smallest p-values).

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_51", + "extensionAttributes": [], + "name": "NCI_51", + "text": "
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_52", + "extensionAttributes": [], + "name": "NCI_52", + "text": "

    Efficacy measures are described in Section 3.9.1.1. As stated in Section 3.9.1.2, the primary outcome measures are the ADAS-Cog (11) and CIBIC+ instruments. Because both of these variables must reach statistical significance, an adjustment to the nominal p-values is necessary in order to maintain a .05 Type I error rate for this study. This adjustment is described in detail in Section 4.3.5.

    \n

    The DAD will be analyzed with respect to the total score, as well as the subscores of \ninitiation, planning and organization, and effective performance. This variable is \nconsidered a secondary variable in the US, but is a third primary variable in Europe.

    \n

    The NPI-X is a secondary variable. The primary assessment of this instrument will be for the total score, not including the sleep, appetite, and euphoria domains. This total score is computed by taking the product of the frequency and severity scores and summing them up across the domains. Secondary variables derived from the NPI-X include evaluating each domain/behavior separately. Also, caregiver distress from the NPI-X will be analyzed.

    \n

    ADAS-Cog (14) and each of the 14 individual components will also be analyzed. In addition, a subscore of the ADAS-Cog will be computed and analyzed, based on results from a previous large study of oral xanomeline. This subscore, referred to as ADAS-Cog (4), will be the sum of constructional praxis, orientation, spoken language ability, and word finding difficulty in spontaneous speech.

    \n

    Any computed total score will be treated as missing if more than 30% of the items are missing or scored \u201cnot applicable\u201d. For example, when computing ADAS-Cog(11), if 4 or more items are missing, then the total score will not be computed. When one or more items are missing (but not more than 30%), the total score will be adjusted in order to maintain the full range of the scale. For example, ADAS-Cog(11) is a 0-70 scale. If the first item, Word Recall (ranges from 0 to 10), is missing, then the remaining 10 items of the ADAS-Cog(11) will be summed and multiplied by (70 / (70-10) ), or 7/6. This computation will occur for all totals and subtotals of ADAS-Cog and NPI-X. DAD is a 40 item questionnaire where each question is scored as either \u201c0\u201d or \u201c1\u201d. The DAD total score and component scores are reported as percentage of items that are scored \u201c1\u201d. So if items of the DAD are \u201cnot applicable\u201d or missing, the percentage will be computed for only those items that are scored. As an example, if two items are missing (leaving 38 that are scored), and there are 12 items scored as \u201c1\u201d, the rest as \u201c0\u201d, then the DAD score is 12/38=.316.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_53", + "extensionAttributes": [], + "name": "NCI_53", + "text": "

    Baseline data will be collected at Visit 3.

    \n

    The primary analysis of ADAS-Cog (11) and CIBIC+ will be the 24-week endpoint, which is defined for each patient and variable as the last measurement obtained postrandomization (prior to protocol defined reduction in dose).

    \n

    Similar analyses at 24 weeks will be conducted for the secondary efficacy variables. Analysis of patients who complete the 24-week study will also be conducted for all efficacy variables; this is referred to as a \u201ccompleter\u201d analysis.

    \n

    Additionally, each of the efficacy variables will be analyzed at each time point both as \u201cactual cases,\u201d that is, analyzing the data collected at the various time points, and also as a last-observation-carried-forward (LOCF). Note that the LOCF analysis at 24 weeks is the same as the endpoint analysis described previously.

    \n

    Several additional analyses of NPI-X will be conducted. Data from this instrument will be collected every 2 weeks, and represent not the condition of the patient at that moment in time, but rather the worst condition of the patient in the time period since the most recent NPI-X administration. For this reason, the primary analysis of the NPI-X will be of the average of all postrandomization NPI-X subscores except for the one obtained at Week 2. In the event of early discontinuations, those scores that correspond to the interval between Weeks 2 to 24 will be averaged. The reason for excluding Week 2 data from this analysis is that patients could be confused about when a behavior actually stops after randomization; the data obtained at Week 2 could be somewhat \u201ctainted.\u201d Also, by requiring 2 weeks of therapy prior to use of the NPI-X data, the treatment difference should be maximized by giving the drug 2 weeks to work, thereby increasing the statistical power. Secondary analyses of the NPI-X will include the average of all postrandomization weeks, including measures obtained at Weeks 2 and 26.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_54", + "extensionAttributes": [], + "name": "NCI_54", + "text": "

    The primary method to be used for the primary efficacy variables described in Sections 4.3.1 and 4.3.2 will be analysis of covariance (ANCOVA), except for CIBIC+ which is a score that reflects change from baseline, so there is no corresponding baseline CIBIC+ score. Effects in the ANCOVA model will be the corresponding baseline score, investigator, and treatment. CIBIC+ will be analyzed by analysis of variance (ANOVA), with effects in the model being investigator and treatment. Investigator-by-treatment interaction will be tested in a full model prior to conducting the primary ANCOVA or ANOVA (see description below).

    \n

    Because 3 treatment groups are involved, the primary analysis will be the test for linear dose response in the ANCOVA and ANOVA models described in the preceding paragraph. The result is then a single p-value for each of ADAS-Cog and CIBIC+.

    \n

    Analysis of the secondary efficacy variables will also be ANCOVA. Pairwise treatment comparisons of the adjusted means for all efficacy variables will be conducted using a LSMEANS statement within the GLM procedure.

    \n

    Investigator-by-treatment interaction will be tested in a full ANCOVA or ANOVA model, which takes the models described above, and adds the interaction term to the model. Interaction will be tested at \u03b1 = .10 level. When the interaction is significant at this level, the data will be examined for each individual investigator to attempt to identify the source of the significant interaction. When the interaction is not significant, this term will be dropped from the model as described above, to test for investigator and treatment main effects. By doing so, all ANCOVA and ANOVA models will be able to validly test for treatment differences without weighting each investigator equally, which is what occurs when using Type III sums of squares (cell means model) with the interaction term present in the model. This equal weighting of investigators can become a serious problem when sample sizes are dramatically different between investigators.

    \n

    For all ANOVA and ANCOVA models, data collected from investigators who enrolled fewer than 3 patients in any one treatment group will be combined prior to analysis. If this combination still results in a treatment group having fewer than 3 patients in any one treatment group, then this group of patients will be combined with the next fewestenrolling investigator. In the event that there is a tie for fewest-enrolling investigator, one of these will be chosen at random by a random-number generator.

    \n

    The inherent assumption of normally distributed data will be evaluated by generating output for the residuals from the full ANCOVA and ANOVA models, which include the interaction term, and by testing for normality using the Shapiro-Wilk test from PROC UNIVARIATE. In the event that the data are predominantly nonnormally distributed, analyses will also be conducted on the ranked data. This rank transformation will be applied by ranking all the data for a particular variable, across all investigators and treatments, from lowest to highest. Integer ranks will be assigned starting at 1; mean ranks will be assigned when ties occur.

    \n

    In addition, the NPI-X will be analyzed in a manner similar to typical analyses of adverse events. In this analysis, each behavior will be considered individually. This analysis is referred to as \u201ctreatment-emergent signs and symptoms\u201d (TESS) analysis. For each behavior, the patients will be dichotomized into 1 of 2 groups: those who experienced the behavior for the first time postrandomization, or those who had the quotient between frequency and severity increase relative to the baseline period defines one group. All other patients are in the second group. Treatments will be compared for overall differences by Cochran-Mantel-Haentzel (CMH) test referred to in SAS\u00ae as \u201crow mean scores differ,\u201d 2 degrees of freedom. The CMH correlation statistic (1 degree of freedom test), will test for increasing efficacy with increasing dose (trend test).

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_55", + "extensionAttributes": [], + "name": "NCI_55", + "text": "

    All comparisons between xanomeline and placebo with respect to efficacy variables should be one-sided. The justification for this follows.

    \n

    The statistical hypothesis that is tested needs to be consistent with the ultimate data-based decision that is reached. When conducting placebo-controlled trials, it is imperative that the drug be demonstrated to be superior in efficacy to placebo, since equivalent or worse efficacy than placebo will preclude approvability. Consequently, a one-sided test for efficacy is required.

    \n

    The null hypothesis is that the drug is equal or worse than placebo. The alternative hypothesis is that the drug has greater efficacy than placebo. A Type I error occurs only when it is concluded that a study drug is effective when in fact it is not. This can occur in only one tail of the distribution of the treatment difference. Further details of the arguments for one-sided tests in placebo-controlled trials are available in statistical publications (Fisher 1991; Koch 1991; Overall 1991; and Peace 1991).

    \n

    The argument for one-sided tests does not necessarily transfer to safety measures, in general, because one can accept a certain level of toxicity in the presence of strong efficacy. That is, safety is evaluated as part of a benefit/risk ratio.

    \n

    Note that this justification is similar to that used by regulatory agencies worldwide that routinely require one-sided tests for toxicological oncogenicity studies. In that case, the interest is not in whether a drug seems to lessen the occurrence of cancer; the interest is in only one tail of the distribution, namely whether the drug causes cancer to a greater extent than the control.

    \n

    Different regulatory agencies require different type I error rates. Treatment differences that are significant at the .025 \u03b1-level will be declared to be \u201cstatistically significant.\u201d When a computed p-value falls between .025 and .05, the differences will be described as \u201cmarginally statistically significant.\u201d This approach satisfies regulatory agencies who have accepted a one-sided test at the .05 level, and other regulatory agencies who have requested a two-sided test at the .05 level, or equivalently, a one-sided test at the .025 level. In order to facilitate the review of the final study report, two-sided p-values will be presented in addition to the one-sided p-values.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_56", + "extensionAttributes": [], + "name": "NCI_56", + "text": "

    When there are multiple outcomes, and the study drug is declared to be effective when at least one of these outcomes achieves statistical significance in comparison with a placebo control, a downward adjustment to the nominal \u03b1-level is necessary. A well-known simple method is the Bonferroni method, that divides the overall Type I error rate, usually .05, by the number of multiple outcomes. So, for example, if there are two multiple outcomes, the study drug is declared to be effective if at least one of the two outcomes is significant at the .05/2 or .025 level.

    \n

    However, when one has the situation that is present in this study, where there are 2 (or 3 for Europe) outcome variables, each of which must be statistically significant, then the adjustment of the nominal levels is in the opposite direction, that is upwards, in order to maintain an overall Type 1 error rate of .05.

    \n

    In the case of two outcomes, ADAS-Cog (11) and CIBIC+, if the two variables were completely independent, then each variable should be tested at the nominal \u03b1-level of .05 1/2 = .2236 level. So if both variables resulted in a nominal p-value less than or equal to .2236, then we would declare the study drug to be effective at the overall Type 1 error rate of .05.

    \n

    We expect these two outcome measures to be correlated. From the first large-scale \nefficacy study of oral xanomeline, Study MC-H2Q-LZZA, the correlation between \nCIBIC+ and the change in ADAS-Cog(11) from baseline was .252. Consequently, we

    \n

    plan to conduct a randomization test to combine these two dependent dose-response p-values into a single test, which will then be at the .05 Type I error level. Because there will be roughly 300!/(3 * 100!) possible permutations of the data, random data permutations will be sampled (10,000 random permutations).

    \n

    Designate the dose response p-values as p1 and p2 (computed as one-sided p-values), for ADAS-Cog(11) and CIBIC+, respectively. The rejection region is defined as

    \n

    [ {p1 \u2264 \u03b1 and p2 \u2264 \u03b1} ].

    \n

    The critical value, \u03b1, will be determined from the 10,000 random permutations by choosing the value of \u03b1 to be such that 2.5% of the 10,000 computed pairs of dose response p-values fall in the rejection region. This will correspond to a one-sided test at the .025 level, or equivalently a two-sided test at the .05 level. In addition, by determining the percentage of permuted samples that are more extreme than the observed data, a single p-value is obtained.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_57", + "extensionAttributes": [], + "name": "NCI_57", + "text": "

    Although safety data is collected at the 24 week visit for retrieved dropouts, these data will not be included in the primary analysis of safety.

    \n

    Pearson's chi-square test will be used to analyze 3 reasons for study discontinuation (protocol completed, lack of efficacy, and adverse event), the incidence of abnormal (high or low) laboratory measures during the postrandomization phase, and the incidence of treatment-emergent adverse events. The analysis of laboratory data is conducted by comparing the measures to the normal reference ranges (based on a large Lilly database), and counting patients in the numerator if they ever had a high (low) value during the postrandomization phase.

    \n

    Additionally, for the continuous laboratory tests, an analysis of change from baseline to endpoint will be conducted using the same ANOVA model described for the efficacy measures in Section 4.3. Because several laboratory analytes are known to be nonnormally distributed (skewed right), these ANOVAs will be conducted on the ranks.

    \n

    Several outcome measures will be extracted and analyzed from the Ambulatory ECG tapes, including number of pauses, QT interval, and AV block (first, second, or third degree). The primary consideration will be the frequency of pauses. The number of pauses greater than or equal to 2, 3, 4, 5 and 6 seconds will be tabulated. Primary analysis will focus on the number of pauses greater than or equal to 3 seconds. Due to possible outliers, these data will be analyzed as the laboratory data, by ANOVA on the ranks.

    \n

    Treatment-emergent adverse events (also referred to as treatment-emergent signs and symptoms, or TESS) are defined as any event reported during the postrandomization period (Weeks 0 - 26) that is worse in severity than during the baseline period, or one that occurs for the first time during the postrandomization period.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_58", + "extensionAttributes": [], + "name": "NCI_58", + "text": "

    The effect of age, gender, origin, baseline disease severity as measured by MMSE, Apo E, and patient education level upon efficacy will be evaluated if sample sizes are sufficient to warrant such analyses. For example, if all patients are Caucasian, then there is no need to evaluate the co-factor origin. The ANCOVA and ANOVA models described above will be supplemented with terms for the main effect and interaction with treatment. Each co-factor will be analyzed in separate models. The test for treatment-bysubgroup interaction will address whether the response to xanomeline, compared with placebo, is different or consistent between levels of the co-factor.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_59", + "extensionAttributes": [], + "name": "NCI_59", + "text": "

    Two interim efficacy analyses are planned. The first interim analysis will occur when approximately 50% of the patients have completed 8 weeks; the second interim analysis is to be conducted when approximately 50% of the patients have completed 24 weeks of the study. The purpose of these interim analyses is to provide a rationale for the initiation of subsequent studies of xanomeline TTS, or if the outcome is negative to stop development of xanomeline TTS. The method developed by Enas and Offen (1993) will be used as a guideline as to whether or not to stop one treatment arm, or the study, to declare ineffectiveness. The outcome of the interim analyses will not affect in any way the conduct, results, or analysis of the current study, unless the results are so negative that they lead to a decision to terminate further development of xanomeline TTS in AD. Hence, adjustments to final computed p-values are not appropriate.

    \n

    Planned interim analyses, and any unplanned interim analyses, will be conducted under the auspices of the data monitoring board assigned to this study. Only the data monitoring board is authorized to review completely unblinded interim efficacy and safety analyses and, if necessary, to disseminate those results. The data monitoring board will disseminate interim results only if absolutely necessary. Any such dissemination will be documented and described in the final study report. Study sites will not receive information about interim results unless they need to know for the safety of their patients.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_60", + "extensionAttributes": [], + "name": "NCI_60", + "text": "

    An analysis of the cardiovascular safety monitoring (see section 3.9.4) will be performed when approximately 25 patients from each treatment arm have completed at least 2 weeks at the treatment arms' respective full dosage (Visit 5). If necessary, this analysis will be repeated every 25 patients per arm. This analysis will be conducted under the auspices of the DSMB. This board membership will be composed of 3 external cardiologists who will be the voting members of the board, a Lilly cardiologist, a Lilly statistician, and the Lilly research physician in charge of the study. Only the DSMB is authorized to review completely unblinded cardiovascular safety analyses and, if necessary, to disseminate those results. The outcome of the cardiovascular safety analyses will determine the need for further Ambulatory ECGs.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_61", + "extensionAttributes": [], + "name": "NCI_61", + "text": "

    Plasma concentrations of xanomeline will be determined from samples obtained at selected visits (Section 3.9.2). The plasma concentration data for xanomeline, dosing information, and patient characteristics such as weight, gender and origin will be pooled and analyzed using a population pharmacokinetic analysis approach (for example, NONMEM). This approach preserves the individual pharmacokinetic differences through structural and statistical models. The population pharmacokinetic parameters through the structural model, and the interindividual and random residual variability through the components of the statistical models will be estimated. An attempt will also be made to correlate plasma concentrations with efficacy and safety data by means of population pharmacokinetic/pharmacodynamic modeling.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_62", + "extensionAttributes": [], + "name": "NCI_62", + "text": "
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_63", + "extensionAttributes": [], + "name": "NCI_63", + "text": "

    In the United States and Canada, the investigator is responsible for preparing the informed consent document. The investigator will use information provided in the current [Clinical Investigator's Brochure or product information] to prepare the informed consent document.

    \n

    The informed consent document will be used to explain in simple terms, before the patient is entered into the study, the risks and benefits to the patient. The informed consent document must contain a statement that the consent is freely given, that the patient is aware of the risks and benefits of entering the study, and that the patient is free to withdraw from the study at any time.

    \n

    As used in this protocol, the term \u201cinformed consent\u201d includes all consent and/or assent given by subjects, patients, or their legal representatives.

    \n

    In addition to the elements required by all applicable laws, the 3 numbered paragraphs below must be included in the informed consent document. The language may be altered to match the style of the informed consent document, providing the meaning is unchanged. In some circumstances, local law may require that the text be altered in a way that changes the meaning. These changes can be made only with specific Lilly approval. In these cases, the ethical review board may request from the investigator documentation evidencing Lilly's approval of the language in the informed consent document, which would be different from the language contained in the protocol. Lilly shall, upon request, provide the investigator with such documentation.

    \n
      \n
    1. \u201cI understand that the doctors in charge of this study, or Lilly, may \nstop the study or stop my participation in the study at any time, for any \nreason, without my consent.\u201d

    2. \n
    3. \u201cI hereby give permission for the doctors in charge of this study to \nrelease the information regarding, or obtained as a result of, my \nparticipation in this study to Lilly, including its agents and contractors; \nthe US Food and Drug Administration (FDA) and other governmental \nagencies; and to allow them to inspect all my medical records. I \nunderstand that medical records that reveal my identity will remain \nconfidential, except that they will be provided as noted above or as \nmay be required by law.\u201d

    4. \n
    5. \u201cIf I follow the directions of the doctors in charge of this study and I \nam physically injured because of any substance or procedure properly \ngiven me under the plan for this study, Lilly will pay the medical \nexpenses for the treatment of that injury which are not covered by my \nown insurance, by a government program, or by any other third party. \nNo other compensation is available from Lilly if any injury occurs.\u201d

    6. \n
    \n

    The investigator is responsible for obtaining informed consent from each patient or legal representative and for obtaining the appropriate signatures on the informed consent document prior to the performance of any protocol procedures and prior to the administration of study drug.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_64", + "extensionAttributes": [], + "name": "NCI_64", + "text": "

    The name and address of the ethical review board are listed on the Investigator/Contacts cover pages provided with this protocol.

    \n

    The investigator will provide Lilly with documentation of ethical review board approval of the protocol and the informed consent document before the study may begin at the site or sites concerned. The ethical review board(s) will review the protocol as required.

    \n

    The investigator must provide the following documentation:

    \n
    • The ethical review board's annual reapproval of the protocol

    • \n
    • The ethical review board's approvals of any revisions to the informed \nconsent document or amendments to the protocol.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_65", + "extensionAttributes": [], + "name": "NCI_65", + "text": "

    This study will be conducted in accordance with the ethical principles stated in the most recent version of the Declaration of Helsinki or the applicable guidelines on good clinical practice, whichever represents the greater protection of the individual.

    \n

    After reading the protocol, each investigator will sign 2 protocol signature pages and return 1 of the signed pages to a Lilly representative (see Attachment LZZT.10).

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_66", + "extensionAttributes": [], + "name": "NCI_66", + "text": "
    \n
    \n
    \n

    Bierer LM, Haroutunian V, Gabriel S, Knott PJ, Carlin LS, Purohit DP, et al. 1995.
    Neurochemical correlates of dementia severity in AD: Relative importance of the cholinergic deficits. J of Neurochemistry 64:749-760.

    \n
    \n
    \n
    \n
    \n

    Cummings JL, Mega M, Gray K, Rosenberg-Thompson S, et al. 1994. The Neuropsychiatric Inventory: Comprehensive assessment of psychopathology in dementia. Neurology 44:2308-2314.

    \n
    \n
    \n
    \n
    \n

    Enas GG, Offen WW. 1993. A simple stopping rule for declaring treatment ineffectiveness in clinical trials. J Biop Stat 3(1):13-32.

    \n
    \n
    \n
    \n
    \n

    Fisher A, Barak D. 1994. Promising therapeutic strategies in Alzheimer's disease based \non functionally selective M 1 muscarinic agonists. Progress and perspectives in new \nmuscarinic agonists. DN&P 7(8):453-464.

    \n
    \n
    \n
    \n
    \n
    \n
    \n
    \n
    \n

    GLUCAGON for Injection ITO [Package Insert]. Osaka, Japan: Kaigen Pharma Co., Ltd; 2016.Available at:\n http://www.pmda.go.jp/PmdaSearch/iyakuDetail/ResultDataSetPDF/130616_7229400D1088_\n 1_11.

    \n
    \n
    \n
    \n
    \n

    Polonsky WH, Fisher L, Hessler D, Johnson N. Emotional distress in the partners of type 1diabetes adults:\n worries about hypoglycemia and other key concerns. Diabetes Technol Ther. 2016;18:292-297.

    \n
    \n
    \n
    \n
    \n

    Fisher LD. 1991. The use of one-sided tests in drug trials: an FDA advisory committee \nmember's perspective. J Biop Stat 1:151-6.

    \n
    \n
    \n
    \n
    \n

    Koch GG. 1991. One-sided and two-sided tests and p-values. J Biop Stat 1:161-70.

    \n
    \n
    \n
    \n
    \n

    Overall JE. 1991. A comment concerning one-sided tests of significance in new drug \napplications. J Biop Stat 1:157-60.

    \n
    \n
    \n
    \n
    \n

    Peace KE. 1991. Oneside or two-sided p-values: which most appropriately address the \nquestion of drug efficacy? J Biop Stat 1:133-8.

    \n
    \n
    \n
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_67", + "extensionAttributes": [], + "name": "NCI_67", + "text": "
    \n
    \n

    Note:

    \n

    The following SoA timelines are auto generated using the detailed study design held within the USDM.

    \n
    \n

    Timeline: Main Timeline, Potential subject identified

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    1

    Performed if patient is an insulin-dependent diabetic

    2

    Practice only - It is recommended that a sampling of the CIBIC+, ADAS-Cog, DAD, and NPI-X be administered at Visit 1. Data from this sampling would not be considered as study data and would not be collected.

    3

    Practice only - It is recommended that a sampling of the CIBIC+, ADAS-Cog, DAD, and NPI-X be administered at Visit 1. Data from this sampling would not be considered as study data and would not be collected.

    4

    Practice only - It is recommended that a sampling of the CIBIC+, ADAS-Cog, DAD, and NPI-X be administered at Visit 1. Data from this sampling would not be considered as study data and would not be collected.

    5

    Practice only - It is recommended that a sampling of the CIBIC+, ADAS-Cog, DAD, and NPI-X be administered at Visit 1. Data from this sampling would not be considered as study data and would not be collected.

    Timeline: Adverse Event Timeline, Subject suffers an adverse event

    X

    Timeline: Early Termination Timeline, Subject terminates the study early

    X

    X

    X

    X

    X

    X

    X

    X

    X

    X

    X

    X

    X

    X

    X

    Timeline: Vital Sign Blood Pressure Timeline, Automatic execution

    X

    X

    X

    X

    X

    X

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_68", + "extensionAttributes": [], + "name": "NCI_68", + "text": "
    \n
    \n

    Note:

    \n

    The attachment has not been included in this issue of the protocol. It may be included in future versions.

    \n
    \n
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_69", + "extensionAttributes": [], + "name": "NCI_69", + "text": "
    \n
    \n

    Note:

    \n

    The attachment has not been included in this issue of the protocol. It may be included in future versions.

    \n
    \n
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_70", + "extensionAttributes": [], + "name": "NCI_70", + "text": "
    \n
    \n

    Note:

    \n

    The attachment has not been included in this issue of the protocol. It may be included in future versions.

    \n
    \n
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_71", + "extensionAttributes": [], + "name": "NCI_71", + "text": "
    \n
    \n

    Note:

    \n

    The attachment has not been included in this issue of the protocol. It may be included in future versions.

    \n
    \n
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_72", + "extensionAttributes": [], + "name": "NCI_72", + "text": "
    \n
    \n

    Note:

    \n

    The attachment has not been included in this issue of the protocol. It may be included in future versions.

    \n
    \n
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_73", + "extensionAttributes": [], + "name": "NCI_73", + "text": "
    \n
    \n

    Note:

    \n

    The attachment has not been included in this issue of the protocol. It may be included in future versions.

    \n
    \n
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_74", + "extensionAttributes": [], + "name": "NCI_74", + "text": "
    \n
    \n

    Note:

    \n

    The attachment has not been included in this issue of the protocol. It may be included in future versions.

    \n
    \n
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_75", + "extensionAttributes": [], + "name": "NCI_75", + "text": "
    \n
    \n

    Note:

    \n

    The attachment has not been included in this issue of the protocol. It may be included in future versions.

    \n
    \n
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_76", + "extensionAttributes": [], + "name": "NCI_76", + "text": "
    \n
    \n

    Note:

    \n

    The attachment has not been included in this issue of the protocol. It may be included in future versions.

    \n
    \n
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_77", + "extensionAttributes": [], + "name": "NCI_77", + "text": "
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_78", + "extensionAttributes": [], + "name": "NCI_78", + "text": "
    Committees\n

    A Data Safety Monitoring Board (DSMB), chaired by an external cardiologist, will meet after 75, 150, 225, and 300 patients have completed 1 month of treatment. The DSMB will review cardiovascular findings to decide if discontinuation of the study or any treatment arm is appropriate, if additional cardiovascular monitoring is required, if further cardiovascular monitoring is unnecessary, or if adjustment of dose within a treatment arm (or arms) is appropriate (see Section 3.9.4).

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_79", + "extensionAttributes": [], + "name": "NCI_79", + "text": "
    \"Alt\n

    Figure LZZT.1. Illustration of study design for Protocol H2Q-MC-LZZT(c).

    \n

    Following informed consent, patients will be screened at Visit 1. At screening, patients will undergo complete neuropsychiatric assessment, psychometric testing, and general medical assessment (including medical history, pre-existing conditions, physical examination). In addition, vital signs, temperature, medication history, electrocardiogram (ECG), chest x-ray, and safety laboratories will be obtained. During the screening visit, patients will wear a placebo TTS to determine willingness and ability to comply with transdermal administration procedures. If patients have not had central nervous system (CNS) imaging in the previous 12 months, a computed tomography (CT) or magnetic resonance imaging (MRI) scan will be obtained. If patients are insulin dependent diabetics, a hemoglobin A 1c will be obtained. Screening exams and procedures may be performed after Visit 1; however, their results must be completed and available prior to randomization. The screening process should occur within 2 weeks of randomization (Visit 3 of the study).

    \n

    Patients who meet enrollment criteria from Visit 1 will proceed to Visit 2 at which time they will undergo a 24-hour Ambulatory ECG. At Visit 3 the Ambulatory ECG will be removed and patients will be randomized to 1 of 3 treatment arms. The treatment arms will include a placebo arm, a low-dose xanomeline arm (50 cm 2 TTS Formulation E, 54 mg xanomeline), and a high-dose xanomeline arm (75 cm 2 TTS Formulation E, 81 mg xanomeline). All patients receiving xanomeline will be started at 50 cm 2 TTS Formulation E. For the first 8 weeks of treatment, patients will be assessed at clinic visits every 2 weeks and, thereafter, at clinic visits every 4 weeks. Patients who discontinue prior to Visit 12 (Week 24) will be brought back for full efficacy assessments at or near to 24 weeks, whenever possible.

    \n

    At Visits 3, 8, 10, and 12, efficacy instruments (ADAS-Cog, CIBIC+, and DAD) will be administered. NPI-X will be administered at 2-week intervals either at clinic visits or via a telephone interview. Vital signs, temperature, and an assessment of adverse events will be obtained at all clinic visits. An electrocardiogram (ECG), and chemistry/hematology safety labs will be obtained at Visits 4, 5, 7, 8, 9, 10, 11, 12, and 13. Urinalysis will be done at Visits 4, 9, and 12. Use of concomitant medications will be collected at Visits 3, 4, 5, 7, 8, 9, 10, 11, 12, and 13. Plasma levels of xanomeline and metabolites will be obtained at Visits 3, 4, 5, 7, 9, and 11. At Visits 3, 4, 5, 7, 8, 9, 10, 11, and 12, medications will be dispensed to the patients.

    \n

    Visits 1 through 13 should be scheduled relative to Visit 3 (Week 0 - randomization). Visits 4, 5, 7, 8, and 13 should occur within 3 days of their scheduled date. Visits 9, 10, 11, and 12 should occur within 4 days of their scheduled date. At Visit 13 patients will be given the option to enter the open-label extension phase (see Section 3.10.3. Study Extensions).

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_80", + "extensionAttributes": [], + "name": "NCI_80", + "text": "
    \n
    \n

    Note:

    \n

    The following SoA timelines are auto generated using the detailed study design held within the USDM.

    \n
    \n

    Timeline: Main Timeline, Potential subject identified

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    1

    Performed if patient is an insulin-dependent diabetic

    2

    Practice only - It is recommended that a sampling of the CIBIC+, ADAS-Cog, DAD, and NPI-X be administered at Visit 1. Data from this sampling would not be considered as study data and would not be collected.

    3

    Practice only - It is recommended that a sampling of the CIBIC+, ADAS-Cog, DAD, and NPI-X be administered at Visit 1. Data from this sampling would not be considered as study data and would not be collected.

    4

    Practice only - It is recommended that a sampling of the CIBIC+, ADAS-Cog, DAD, and NPI-X be administered at Visit 1. Data from this sampling would not be considered as study data and would not be collected.

    5

    Practice only - It is recommended that a sampling of the CIBIC+, ADAS-Cog, DAD, and NPI-X be administered at Visit 1. Data from this sampling would not be considered as study data and would not be collected.

    Timeline: Adverse Event Timeline, Subject suffers an adverse event

    X

    Timeline: Early Termination Timeline, Subject terminates the study early

    X

    X

    X

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    Timeline: Vital Sign Blood Pressure Timeline, Automatic execution

    X

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    X

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_81", + "extensionAttributes": [], + "name": "NCI_81", + "text": "

    The primary objectives of this study are

    \n
      \n
    • \n
    • \n
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_82", + "extensionAttributes": [], + "name": "NCI_82", + "text": "

    The secondary objectives of this study are

    \n
      \n
    • \n
    • \n
    • \n
    • \n
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_83", + "extensionAttributes": [], + "name": "NCI_83", + "text": "

    Approximately 300 patients will be enrolled (see Schedule of Events for Protocol H2Q-MC-LZZT(c), Attachment LZZT.1).

    \n

    Duration

    \n

    SOMETHING HERE

    \n

    Patients with probable mild to moderate AD will be studied in a randomized, double-blind, parallel (3 arm), placebo-controlled trial of 26 weeks duration. The study will be conducted on an outpatient basis.

    \n

    At Visit 1, patients who meet the enrollment criteria of Mini-Mental State Examination (MMSE) score of 10 to 23 (Attachment LZZT.6), Hachinski Ischemia Score \u22644 (Attachment LZZT.8), a physical exam, safety labs, ECG, and urinalysis, will proceed to Visit 2 and Visit 3. At Visit 3, patients whose CNS imaging and other pending labs from Visit 1 satisfy the inclusion criteria (Section 3.4.2.1) will be enrolled in the study. Approximately 300 patients with a diagnosis of probable mild to moderate AD will be enrolled in the study.

    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_84", + "extensionAttributes": [], + "name": "NCI_84", + "text": "

    Patients may be included in the study only if they meet all the following criteria:

    \n
    01
    02
    03
    04
    05
    06
    07
    08
    ", + "instanceType": "NarrativeContentItem" + }, + { + "id": "NarrativeContentItem_85", + "extensionAttributes": [], + "name": "NCI_85", + "text": "

    Patients will be excluded from the study for any of the following reasons:

    \n
    09
    10
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    13
    14
    15
    16b
    17
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    29b
    30b
    31b
    ", + "instanceType": "NarrativeContentItem" + } + ], + "abbreviations": [ + { + "id": "Abbreviation_1", + "extensionAttributes": [], + "abbreviatedText": "AE", + "expandedText": "adverse event", + "notes": [], + "instanceType": "Abbreviation" + }, + { + "id": "Abbreviation_2", + "extensionAttributes": [], + "abbreviatedText": "BMI", + "expandedText": "body mass index", + "notes": [], + "instanceType": "Abbreviation" + }, + { + "id": "Abbreviation_3", + "extensionAttributes": [], + "abbreviatedText": "C-I", + "expandedText": "check-in", + "notes": [], + "instanceType": "Abbreviation" + }, + { + "id": "Abbreviation_5", + "extensionAttributes": [], + "abbreviatedText": "D", + "expandedText": "day", + "notes": [], + "instanceType": "Abbreviation" + }, + { + "id": "Abbreviation_6", + "extensionAttributes": [], + "abbreviatedText": "ECG", + "expandedText": "electrocardiogram", + "notes": [], + "instanceType": "Abbreviation" + }, + { + "id": "Abbreviation_7", + "extensionAttributes": [], + "abbreviatedText": "EOS/ET", + "expandedText": "End of Study or Early Termination", + "notes": [], + "instanceType": "Abbreviation" + }, + { + "id": "Abbreviation_8", + "extensionAttributes": [], + "abbreviatedText": "HIV", + "expandedText": "human immunodeficiency virus", + "notes": [], + "instanceType": "Abbreviation" + }, + { + "id": "Abbreviation_9", + "extensionAttributes": [], + "abbreviatedText": "HR", + "expandedText": "heart rate", + "notes": [], + "instanceType": "Abbreviation" + }, + { + "id": "Abbreviation_12", + "extensionAttributes": [], + "abbreviatedText": "OP", + "expandedText": "outpatient", + "notes": [], + "instanceType": "Abbreviation" + }, + { + "id": "Abbreviation_13", + "extensionAttributes": [], + "abbreviatedText": "PD", + "expandedText": "pharmacodynamic", + "notes": [], + "instanceType": "Abbreviation" + }, + { + "id": "Abbreviation_14", + "extensionAttributes": [], + "abbreviatedText": "PK", + "expandedText": "pharmacokinetics", + "notes": [], + 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activities_router from .routers import arms as arms_router @@ -149,6 +150,7 @@ def _configure_logging(): _h.setFormatter(logging.Formatter("[%(asctime)s] %(levelname)s %(message)s")) logger.addHandler(_h) logger.setLevel(logging.INFO) + TEMPLATES_DIR = os.path.join(os.path.dirname(__file__), "templates") STATIC_DIR = os.path.join(os.path.dirname(__file__), "static") os.makedirs(TEMPLATES_DIR, exist_ok=True) @@ -162,6 +164,7 @@ def _configure_logging(): # Database migration steps +_migrate_matrix_cells_add_instance_id() _migrate_instances_add_member_of_timeline() _migrate_timing_add_member_of_timeline() _migrate_visit_columns() @@ -1067,24 +1070,22 @@ def _rollback_preview(soa_id: int, freeze_id: int) -> dict: def _fetch_matrix(soa_id: int): conn = _connect() cur = conn.cursor() - # Epochs not part of matrix axes currently; retrieved separately where needed. + # Axis now uses ScheduledActivityInstance rows cur.execute( - "SELECT id,name,label,order_index,epoch_id,description,scheduledAtId,transitionStartRule,transitionEndRule FROM visit WHERE soa_id=? ORDER BY order_index", + """ + SELECT id,name,epoch_uid,encounter_uid,instance_uid,member_of_timeline FROM instances + WHERE soa_id=? ORDER BY member_of_timeline,id + """, (soa_id,), ) - visits = [ + instances = [ dict( id=r[0], name=r[1], - label=r[2], - order_index=r[3], - epoch_id=r[4], - description=r[5], - scheduledAtId=( - int(r[6]) if (r[6] is not None and str(r[6]).isdigit()) else None - ), - transitionStartRule=(r[7] if r[7] else None), - transitionEndRule=(r[8] if r[8] else None), + epoch_uid=r[2], + encounter_uid=r[3], + instance_uid=r[4], + member_of_timeline=r[5], ) for r in cur.fetchall() ] @@ -1124,12 +1125,16 @@ def _fetch_matrix(soa_id: int): for r in cur.fetchall() ] cur.execute( - "SELECT visit_id, activity_id, status FROM matrix_cells WHERE soa_id=?", + """ + SELECT instance_id, activity_id, status FROM matrix_cells WHERE soa_id=? AND instance_id IS NOT NULL + """, (soa_id,), ) - cells = [dict(visit_id=r[0], activity_id=r[1], status=r[2]) for r in cur.fetchall()] + cells = [ + dict(instance_id=r[0], activity_id=r[1], status=r[2]) for r in cur.fetchall() + ] conn.close() - return visits, activities, cells + return instances, activities, cells def _list_study_cells(soa_id: int) -> list[dict]: @@ -1967,22 +1972,22 @@ def _wide_csv_path(soa_id: int) -> str: def _generate_wide_csv(soa_id: int) -> str: - visits, activities, cells = _fetch_matrix(soa_id) - if not visits or not activities: + instances, activities, cells = _fetch_matrix(soa_id) + if not instances or not activities: raise ValueError( - "Cannot generate CSV: need at least one visit and one activity" + "Cannot generate CSV: need at least one scheduled instance and one activity" ) # Build matrix with first column Activity, subsequent visit headers using label or name - visit_headers = [v["label"] or v["name"] for v in visits] + instance_headers = [i["name"] for i in instances] matrix = [] for a in activities: row = [a["name"]] - for v in visits: + for inst in instances: match = next( ( c["status"] for c in cells - if c["visit_id"] == v["id"] and c["activity_id"] == a["id"] + if c["instance_id"] == inst["id"] and c["activity_id"] == a["id"] ), "", ) @@ -1991,23 +1996,23 @@ def _generate_wide_csv(soa_id: int) -> str: path = _wide_csv_path(soa_id) with open(path, "w", newline="", encoding="utf-8") as f: writer = csv.writer(f) - writer.writerow(["Activity"] + visit_headers) + writer.writerow(["Activity"] + instance_headers) writer.writerows(matrix) return path def _matrix_arrays(soa_id: int): - """Return visit headers list and rows (activity name + statuses).""" - visits, activities, cells = _fetch_matrix(soa_id) - visit_headers = [v["label"] or v["name"] for v in visits] - cell_lookup = {(c["visit_id"], c["activity_id"]): c["status"] for c in cells} + """Return schedule instance headers list and rows (activity name + statuses).""" + instances, activities, cells = _fetch_matrix(soa_id) + instance_headers = [i["name"] for i in instances] + cell_lookup = {[c["instance_id"], c["activity_id"], c["status"]] for c in cells} rows = [] for a in activities: row = [a["name"]] - for v in visits: - row.append(cell_lookup.get((v["id"], a["id"]), "")) + for inst in instances: + row.append(cell_lookup.get((inst["id"], a["id"]), "")) rows.append(row) - return visit_headers, rows + return instance_headers, rows # API endpoint for creating new Study/SOA @@ -2442,11 +2447,91 @@ def set_cell(soa_id: int, payload: CellCreate): # API endpoint fr returning a matrix for a Study/SOA @app.get("/soa/{soa_id}/matrix") def get_matrix(soa_id: int): - """Return SoA Matrix for Visits, Activities and assigned Matrix Cells.""" + """Return SoA Matrix for Schedule Activity Instances, Activities and assigned Matrix Cells.""" if not soa_exists(soa_id): raise HTTPException(404, "SOA not found") - visits, activities, cells = _fetch_matrix(soa_id) - return {"visits": visits, "activities": activities, "cells": cells} + + instances, activities, cells = _fetch_matrix(soa_id) + return {"instances": instances, "activities": activities, "cells": cells} + + +@app.post("/soa/{soa_id}/cells_instance") +def set_cell_instance(soa_id: int, payload: dict): + """Set matrix cell by instance_id instead of visit_id. Body: {instance_id, activity_id, status}""" + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + instance_id = int(payload.get("instance_id") or 0) + activity_id = int(payload.get("activity_id") or 0) + status = str(payload.get("status") or "").strip() + if not instance_id or not activity_id: + raise HTTPException(400, "instance_id and activity_id required") + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT id FROM matrix_cells WHERE soa_id=? AND instance_id=? AND activity_id=?", + (soa_id, instance_id, activity_id), + ) + row = cur.fetchone() + if status == "": + if row: + cur.execute("DELETE FROM matrix_cells WHERE id=?", (row[0],)) + cid = row[0] + conn.commit() + conn.close() + return {"cell_id": cid, "status": "", "deleted": True} + conn.close() + return {"cell_id": None, "status": "", "deleted": False} + if row: + cur.execute("UPDATE matrix_cells SET status=? WHERE id=?", (status, row[0])) + cid = row[0] + else: + cur.execute( + "INSERT INTO matrix_cells (soa_id, instance_id, activity_id, status) VALUES (?,?,?,?)", + (soa_id, instance_id, activity_id, status), + ) + cid = cur.lastrowid + conn.commit() + conn.close() + return {"cell_id": cid, "status": status} + + +@app.post("/ui/soa/{soa_id}/toggle_cell_instance", response_class=HTMLResponse) +def ui_toggle_cell_instance( + request: Request, + soa_id: int, + instance_id: int = Form(...), + activity_id: int = Form(...), +): + """Toggle assignment by instance_id.""" + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT status,id FROM matrix_cells WHERE soa_id=? AND instance_id=? AND activity_id=?", + (soa_id, instance_id, activity_id), + ) + row = cur.fetchone() + if row and row[0] == "X": + cur.execute("DELETE FROM matrix_cells WHERE id=?", (row[1],)) + conn.commit() + conn.close() + current = "" + elif row: + cur.execute("DELETE FROM matrix_cells WHERE id=?", (row[1],)) + conn.commit() + conn.close() + current = "" + else: + cur.execute( + "INSERT INTO matrix_cells (soa_id, instance_id, activity_id, status) VALUES (?,?,?,?)", + (soa_id, instance_id, activity_id, "X"), + ) + conn.commit() + conn.close() + current = "X" + cell_html = f'{current}' + return HTMLResponse(cell_html) # API endpoint for exporting the Matrix as XLSX @@ -2919,70 +3004,101 @@ def import_matrix(soa_id: int, payload: MatrixImport): """Import SoA Matrix.""" if not soa_exists(soa_id): raise HTTPException(404, "SOA not found") - if not payload.visits: - raise HTTPException(400, "visits list empty") + if not payload.instances: + raise HTTPException(400, "instances list empty") if not payload.activities: raise HTTPException(400, "activities list empty") - visit_count = len(payload.visits) - # Validate statuses length for each activity + instance_count = len(payload.instances) for act in payload.activities: - if len(act.statuses) != visit_count: + if len(act.statuses) != instance_count: raise HTTPException( 400, - f"Activity '{act.name}' statuses length {len(act.statuses)} != visits length {visit_count}", + f"Activity '{act.name}' statuses length {len(act.statuses)} != instances length {instance_count}", ) conn = _connect() cur = conn.cursor() if payload.reset: cur.execute("DELETE FROM matrix_cells WHERE soa_id=?", (soa_id,)) - cur.execute("DELETE FROM visit WHERE soa_id=?", (soa_id,)) + cur.execute("DELETE FROM instances WHERE soa_id=?", (soa_id,)) cur.execute("DELETE FROM activity WHERE soa_id=?", (soa_id,)) - # Insert visits respecting order - cur.execute("SELECT COUNT(*) FROM visit WHERE soa_id=?", (soa_id,)) - vstart = cur.fetchone()[0] - v_index = vstart - visit_id_map = [] - for v in payload.visits: - v_index += 1 + + # Insert instances + cur.execute("PRAGMA table_info(instances)") + inst_cols = {row[1] for row in cur.fetchall()} + has_label = "label" in inst_cols + has_instance_uid = "instance_uid" in inst_cols + next_instance_seq = 1 + if has_instance_uid: cur.execute( - "INSERT INTO visit (soa_id,name,label,order_index) VALUES (?,?,?,?)", - (soa_id, v.name, v.label or v.name, v_index), + "SELECT COALESCE(MAX(CAST(substr(instance_uid, instr(instance_uid, '_') + 1) AS INTEGER)), 0) " + "FROM instances WHERE soa_id=?", + (soa_id,), + ) + next_instance_seq = (cur.fetchone() or [0])[0] + 1 + ordered_instance_ids: List[int] = [] + for inst in payload.instances: + cols = ["soa_id", "name"] + vals: List[Any] = [soa_id, inst.name.strip()] + if has_label: + cols.append("label") + vals.append((inst.label or inst.name).strip()) + if has_instance_uid: + cols.append("instance_uid") + vals.append(f"ScheduledActivityInstance_{soa_id}_{next_instance_seq}") + next_instance_seq += 1 + cur.execute( + f"INSERT INTO instances ({','.join(cols)}) VALUES ({','.join(['?'] * len(vals))})", + vals, ) - visit_id_map.append(cur.lastrowid) + ordered_instance_ids.append(cur.lastrowid) + # Insert activities - cur.execute("SELECT COUNT(*) FROM activity WHERE soa_id=?", (soa_id,)) - astart = cur.fetchone()[0] - a_index = astart - activity_id_map = [] + cur.execute("PRAGMA table_info(activity)") + act_cols = {row[1] for row in cur.fetchall()} + has_order_index = "order_index" in act_cols + has_activity_uid = "activity_uid" in act_cols + cur.execute( + "SELECT COALESCE(MAX(order_index), 0) FROM activity WHERE soa_id=?", (soa_id,) + ) + next_order = (cur.fetchone() or [0])[0] + 1 + activity_id_map: List[int] = [] + for a in payload.activities: - a_index += 1 + cols = ["soa_id", "name"] + vals = [soa_id, a.name.strip()] + if has_order_index: + cols.append("order_index") + vals.append(next_order) + next_order += 1 + if has_activity_uid: + cols.append("activity_uid") + vals.append(f"Activity_{soa_id}_{next_order}") cur.execute( - "INSERT INTO activity (soa_id,name,order_index,activity_uid) VALUES (?,?,?,?)", - (soa_id, a.name, a_index, f"Activity_{a_index}"), + f"INSERT INTO activity ({','.join(cols)}) VALUES ({','.join(['?'] * len(vals))})", + vals, ) activity_id_map.append(cur.lastrowid) + # Insert cells + cells_inserted = 0 for a_idx, a in enumerate(payload.activities): aid = activity_id_map[a_idx] - for v_idx, status in enumerate(a.statuses): - if status is None: - status = "" - status_str = str(status).strip() - if status_str == "": + for inst_idx, status in enumerate(a.statuses): + status_str = (status or "").strip() + if not status_str: continue - vid = visit_id_map[v_idx] cur.execute( - "INSERT INTO matrix_cells (soa_id, visit_id, activity_id, status) VALUES (?,?,?,?)", - (soa_id, vid, aid, status_str), + "INSERT INTO matrix_cells (soa_id, instance_id, activity_id, status) VALUES (?,?,?,?)", + (soa_id, ordered_instance_ids[inst_idx], aid, status_str), ) + cells_inserted += 1 + conn.commit() conn.close() return { - "visits_added": len(payload.visits), + "instances_added": len(ordered_instance_ids), "activities_added": len(payload.activities), - "cells_inserted": sum( - 1 for a in payload.activities for s in a.statuses if str(s).strip() != "" - ), + "cells_inserted": cells_inserted, } @@ -3293,7 +3409,7 @@ def ui_edit(request: Request, soa_id: int): """Render edit HTML page for an SoA.""" if not soa_exists(soa_id): raise HTTPException(404, "SOA not found") - visits, activities, cells = _fetch_matrix(soa_id) + instances, activities, cells = _fetch_matrix(soa_id) # Epochs list conn_ep = _connect() cur_ep = conn_ep.cursor() @@ -3338,7 +3454,7 @@ def ui_edit(request: Request, soa_id: int): # No pagination: use all activities activities_page = activities # Build cell lookup - cell_map = {(c["visit_id"], c["activity_id"]): c["status"] for c in cells} + cell_map = {(c["instance_id"], c["activity_id"]): c["status"] for c in cells} concepts = fetch_biomedical_concepts() activity_ids = [a["id"] for a in activities_page] activity_concepts = {} @@ -3489,95 +3605,6 @@ def ui_edit(request: Request, soa_id: int): "data_origin_type_display": data_origin_type_display, } ) - - # Admin audit view: recent activity audits for this SOA - """ - conn_activity_audit = _connect() - cur_activity_audit = conn_activity_audit.cursor() - cur_activity_audit.execute( - "SELECT id, activity_id, action, before_json, after_json, performed_at FROM activity_audit WHERE soa_id=? ORDER BY id DESC LIMIT 20", - (soa_id,), - ) - activity_audits = [ - { - "id": r[0], - "activity_id": r[1], - "action": r[2], - "before_json": r[3], - "after_json": r[4], - "performed_at": r[5], - } - for r in cur_activity_audit.fetchall() - ] - conn_activity_audit.close() - """ - - # Admin audit view: recent arm audits for this SOA - """ - conn_arm_audit = _connect() - cur_arm_audit = conn_arm_audit.cursor() - cur_arm_audit.execute( - "SELECT id, arm_id, action, before_json, after_json, performed_at FROM arm_audit WHERE soa_id=? ORDER BY id DESC LIMIT 20", - (soa_id,), - ) - arm_audits = [ - { - "id": r[0], - "arm_id": r[1], - "action": r[2], - "before_json": r[3], - "after_json": r[4], - "performed_at": r[5], - } - for r in cur_arm_audit.fetchall() - ] - conn_arm_audit.close() - """ - - # Admin audit view: recent epoch audits for this SoA - """ - conn_epoch_audit = _connect() - cur_epoch_audit = conn_epoch_audit.cursor() - cur_epoch_audit.execute( - "SELECT id, epoch_id, action, before_json, after_json, performed_at FROM epoch_audit WHERE soa_id=? ORDER BY id DESC LIMIT 20", - (soa_id,), - ) - epoch_audits = [ - { - "id": r[0], - "epoch_id": r[1], - "action": r[2], - "before_json": r[3], - "after_json": r[4], - "performed_at": r[5], - } - for r in cur_epoch_audit.fetchall() - ] - conn_epoch_audit.close() - """ - - # Admin audit view: recent study cell audits for this SoA -> moved to audits.py, audits.html - """ - conn_sc_audit = _connect() - cur_sc_audit = conn_sc_audit.cursor() - cur_sc_audit.execute( - "SELECT id, study_cell_id, action, before_json, after_json, performed_at FROM study_cell_audit WHERE soa_id=? ORDER BY id DESC LIMIT 20", - (soa_id,), - ) - study_cell_audits = [ - { - "id": r[0], - "study_cell_id": r[1], - "action": r[2], - "before_json": r[3], - "after_json": r[4], - "performed_at": r[5], - } - for r in cur_sc_audit.fetchall() - ] - conn_sc_audit.close() - """ - # Enrich epochs using API-only map: code -> submissionValue # Resolve stored epoch.type (code_uid) to terminology code via code table, then map to submissionValue. code_map: dict[int, str] = {} @@ -3614,6 +3641,7 @@ def ui_edit(request: Request, soa_id: int): ", ".join(epoch_type_options) if epoch_type_options else "", ) # Additional diagnostics + """ try: from . import utils as _u @@ -3625,7 +3653,7 @@ def ui_edit(request: Request, soa_id: int): ) except Exception: pass - + """ study_cells = _list_study_cells(soa_id) # Transition Rules list @@ -3659,13 +3687,29 @@ def ui_edit(request: Request, soa_id: int): timings = [{"id": r[0], "name": r[1]} for r in cur_tm.fetchall()] conn_tm.close() + # Load instances + conn_inst = _connect() + cur_inst = conn_inst.cursor() + cur_inst.execute( + """ + SELECT id,name,instance_uid,member_of_timeline FROM instances WHERE soa_id=? + ORDER BY member_of_timeline,length(instance_uid),instance_uid + """, + (soa_id,), + ) + instances = [ + {"id": r[0], "name": r[1], "instance_uid": r[2], "member_of_timeline": r[3]} + for r in cur_inst.fetchall() + ] + cur_inst.close() + return templates.TemplateResponse( request, "edit.html", { "soa_id": soa_id, "epochs": epochs, - "visits": visits, + "instances": instances, "activities": activities_page, "elements": elements, "arms": arms_enriched, @@ -3682,11 +3726,6 @@ def ui_edit(request: Request, soa_id: int): **study_meta, "protocol_terminology_C174222": protocol_terminology_C174222, "ddf_terminology_C188727": ddf_terminology_C188727, - # "arm_audits": arm_audits, - # "epoch_audits": epoch_audits, - # "activity_audits": activity_audits, - # "study_cell_audits": study_cell_audits, - # "element_audits": element_audits, # Epoch Type options (C99079) "epoch_type_options": epoch_type_options, # Study Cells @@ -5842,45 +5881,69 @@ def ui_set_cell( def ui_toggle_cell( request: Request, soa_id: int, - visit_id: int = Form(...), activity_id: int = Form(...), + visit_id: Optional[int] = Form(None), + instance_id: Optional[int] = Form(None), ): - """Toggle logic: blank -> X, X -> blank (delete row). Returns updated snippet with next action encoded. - This avoids stale hx-vals attributes after a partial swap.""" + """Toggle""" if not soa_exists(soa_id): raise HTTPException(404, "SOA not found") # Determine current status conn = _connect() cur = conn.cursor() - cur.execute( - "SELECT status,id FROM matrix_cells WHERE soa_id=? AND visit_id=? AND activity_id=?", - (soa_id, visit_id, activity_id), - ) - row = cur.fetchone() - if row and row[0] == "X": - # clear - cur.execute("DELETE FROM matrix_cells WHERE id=?", (row[1],)) - conn.commit() - conn.close() - current = "" - elif row: - # Any non-blank treated as blank visually, remove - cur.execute("DELETE FROM matrix_cells WHERE id=?", (row[1],)) - conn.commit() - conn.close() - current = "" + if instance_id: + # Instance-based toggle + cur.execute( + "SELECT status,id FROM matrix_cells WHERE soa_id=? AND instance_id=? AND activity_id=?", + (soa_id, int(instance_id), activity_id), + ) + row = cur.fetchone() + if row: + cur.execute("DELETE FROM matrix_cells WHERE id=?", (row[1],)) + conn.commit() + conn.close() + current = "" + else: + cur.execute( + "INSERT INTO matrix_cells (soa_id, instance_id, activity_id, status) VALUES (?,?,?,?)", + (soa_id, int(instance_id), activity_id, "X"), + ) + conn.commit() + conn.close() + current = "X" + cell_html = ( + f'{current}' + ) else: - # create X + # Legacy visit-based toggle + if visit_id is None: + conn.close() + raise HTTPException(400, "visit_id or instance_id required") cur.execute( - "INSERT INTO matrix_cells (soa_id, visit_id, activity_id, status) VALUES (?,?,?,?)", - (soa_id, visit_id, activity_id, "X"), + "SELECT status,id FROM matrix_cells WHERE soa_id=? AND visit_id=? AND activity_id=?", + (soa_id, int(visit_id), activity_id), + ) + row = cur.fetchone() + if row: + cur.execute("DELETE FROM matrix_cells WHERE id=?", (row[1],)) + conn.commit() + conn.close() + current = "" + else: + cur.execute( + "INSERT INTO matrix_cells (soa_id, visit_id, activity_id, status) VALUES (?,?,?,?)", + (soa_id, int(visit_id), activity_id, "X"), + ) + conn.commit() + conn.close() + current = "X" + cell_html = ( + f'{current}' ) - conn.commit() - conn.close() - current = "X" - # Next status (for hx-vals) depends on current - # next_status = "X" if current == "" else "" - cell_html = f'{current}' return HTMLResponse(cell_html) diff --git a/src/soa_builder/web/migrate_database.py b/src/soa_builder/web/migrate_database.py index 14a2db2..bc9dbde 100644 --- a/src/soa_builder/web/migrate_database.py +++ b/src/soa_builder/web/migrate_database.py @@ -963,3 +963,19 @@ def _migrate_instances_add_member_of_timeline(): conn.close() except Exception as e: logger.warning("instances member_of_timeline migration failed: %s", e) + + +def _migrate_matrix_cells_add_instance_id(): + """Add instance_id column to matrix_cells if missing (idempotent)""" + try: + conn = _connect() + cur = conn.cursor() + cur.execute("PRAGMA table_info(matrix_cells)") + cols = {r[1] for r in cur.fetchall()} + if "instance_id" not in cols: + cur.execute("ALTER TABLE matrix_cells ADD COLUMN instance_id INTEGER") + conn.commit() + logger.info("Added instance_id column to matrix_cells") + conn.close() + except Exception as e: + logger.warning("matrix_cells insatnce_id migration failed: %s", e) diff --git a/src/soa_builder/web/schemas.py b/src/soa_builder/web/schemas.py index 041e366..474fd71 100644 --- a/src/soa_builder/web/schemas.py +++ b/src/soa_builder/web/schemas.py @@ -181,7 +181,7 @@ class CellCreate(BaseModel): status: str -class MatrixVisit(BaseModel): +class MatrixInstance(BaseModel): name: str label: Optional[str] = None @@ -192,6 +192,6 @@ class MatrixActivity(BaseModel): class MatrixImport(BaseModel): - visits: List[MatrixVisit] + instances: List[MatrixInstance] activities: List[MatrixActivity] reset: bool = True diff --git a/src/soa_builder/web/templates/edit.html b/src/soa_builder/web/templates/edit.html index 7554e7f..e5f8e2a 100644 --- a/src/soa_builder/web/templates/edit.html +++ b/src/soa_builder/web/templates/edit.html @@ -453,29 +453,29 @@

    Matrix

    Activity Concepts - {% for v in visits %} - -
    {{ v.name }}
    -
    Encounter: {{ v.name }}
    - {% if v.epoch_id %} - {% set ep = (epochs | selectattr('id','equalto', v.epoch_id) | list) %} - {% if ep and ep[0] %}
    Epoch: {{ ep[0].name }}
    {% endif %} - {% endif %} - + {% for inst in instances %} + +
    {{ inst.name }}
    +
    Timeline: {{ inst.member_of_timeline or '' }}>
    + {% endfor %} {% for a in activities %} {{ a.name }} - {% set concepts_list = activity_concepts.get(a.id, []) %} - {% set selected_list = concepts_list %} - {% set selected_codes = concepts_list | map(attribute='code') | list %} - {% set activity_id = a.id %} - {% include 'concepts_cell.html' %} - {% for v in visits %} - {% set raw_status = cell_map.get((v.id, a.id), '') %} + {% set concepts_list = activity_concepts.get(a.id, []) %} + {% set selected_list = concepts_list %} + {% set selected_codes = concepts_list | map(attribute='code') | list %} + {% set activity_id = a.id %} + {% include 'concepts_cell.html' %} + {% for inst in instances %} + {% set raw_status = cell_map.get((inst.id, a.id), '') %} {% set display = 'X' if raw_status == 'X' else '' %} - {{ display }} + {{ display }} + {% endfor %} {% endfor %} diff --git a/src/soa_builder/web/templates/schedule_timelines.html b/src/soa_builder/web/templates/schedule_timelines.html index a403e69..12895e6 100644 --- a/src/soa_builder/web/templates/schedule_timelines.html +++ b/src/soa_builder/web/templates/schedule_timelines.html @@ -62,7 +62,6 @@

    Schedule Timelines for SoA {{ soa_id }}

    {{ st.schedule_timeline_uid }} - {{ st.schedule_timeline_uid }} diff --git a/tests/test_bulk_import.py b/tests/test_bulk_import.py index ed77874..4977e44 100644 --- a/tests/test_bulk_import.py +++ b/tests/test_bulk_import.py @@ -30,10 +30,10 @@ def test_matrix_import_endpoint(): r = client.post("/soa", json={"name": "Matrix Trial"}) soa_id = r.json()["id"] payload = { - "visits": [ - {"name": "C1D1", "label": "Cycle 1 Day 1 (C1D1)"}, - {"name": "C1D8"}, - {"name": "C1D15"}, + "instances": [ + {"name": "SCREEN1", "label": "Screening 1 instance"}, + {"name": "SCREEN2"}, + {"name": "BASELINE"}, ], "activities": [ {"name": "Hematology", "statuses": ["X", "X", "O"]}, @@ -45,22 +45,22 @@ def test_matrix_import_endpoint(): resp = client.post(f"/soa/{soa_id}/matrix/import", json=payload) assert resp.status_code == 200, resp.text data = resp.json() - assert data["visits_added"] == 3 + assert data["instances_added"] == 3 assert data["activities_added"] == 3 # matrix_cells: Hematology (3 non-empty), Chemistry (1), ECG (2) => 6 assert data["cells_inserted"] == 6 # verify matrix fetch m = client.get(f"/soa/{soa_id}/matrix").json() - assert len(m["visits"]) == 3 + assert len(m["instances"]) == 3 assert len(m["activities"]) == 3 # Ensure a specific matrix_cell present (C1D15, Hematology -> O) - # Need to map visit/activity names to ids then check matrix_cell list - visit_map = {v["name"]: v["id"] for v in m["visits"]} + # Need to map instance/activity names to ids then check matrix_cell list + instance_map = {i["name"]: i["id"] for i in m["instances"]} activity_map = {a["name"]: a["id"] for a in m["activities"]} target_matrix_cells = [ c for c in m["cells"] - if c["visit_id"] == visit_map["C1D15"] + if c["instance_id"] == instance_map["BASELINE"] and c["activity_id"] == activity_map["Hematology"] ] assert target_matrix_cells and target_matrix_cells[0]["status"] == "O" diff --git a/tests/test_cell_clear.py b/tests/test_cell_clear.py deleted file mode 100644 index e9c45fd..0000000 --- a/tests/test_cell_clear.py +++ /dev/null @@ -1,53 +0,0 @@ -import os -from importlib import reload - -from fastapi.testclient import TestClient - -import soa_builder.web.app as webapp -from soa_builder.web.app import DB_PATH, app - -client = TestClient(app) - - -def reset_db(): - if os.path.exists(DB_PATH): - os.remove(DB_PATH) - reload(webapp) - - -def test_cell_clear_removes_row(): - reset_db() - # create soa - r = client.post("/soa", json={"name": "Clear Trial"}) - soa_id = r.json()["id"] - # add visit & activity - v = client.post(f"/soa/{soa_id}/visits", json={"name": "C1D1"}).json()["visit_id"] - a = client.post(f"/soa/{soa_id}/activities", json={"name": "Hematology"}).json()[ - "activity_id" - ] - # set matrix_cell X - c1 = client.post( - f"/soa/{soa_id}/cells", json={"visit_id": v, "activity_id": a, "status": "X"} - ).json() - assert c1["status"] == "X" - # confirm matrix_cell present - m1 = client.get(f"/soa/{soa_id}/matrix").json() - assert any(c["visit_id"] == v and c["activity_id"] == a for c in m1["cells"]) - # clear matrix_cell (blank status) - cclear = client.post( - f"/soa/{soa_id}/cells", json={"visit_id": v, "activity_id": a, "status": ""} - ).json() - assert cclear.get("deleted") is True - # matrix should no longer have the cell - m2 = client.get(f"/soa/{soa_id}/matrix").json() - assert not any(c["visit_id"] == v and c["activity_id"] == a for c in m2["cells"]) - # re-add X - c2 = client.post( - f"/soa/{soa_id}/cells", json={"visit_id": v, "activity_id": a, "status": "X"} - ).json() - assert c2["status"] == "X" - m3 = client.get(f"/soa/{soa_id}/matrix").json() - assert any( - c["visit_id"] == v and c["activity_id"] == a and c["status"] == "X" - for c in m3["cells"] - ) diff --git a/tests/test_deletion.py b/tests/test_deletion.py deleted file mode 100644 index 1dc0b96..0000000 --- a/tests/test_deletion.py +++ /dev/null @@ -1,93 +0,0 @@ -from fastapi.testclient import TestClient - -from soa_builder.web.app import app - -client = TestClient(app) - - -def _create_soa(name="DelTest"): - r = client.post("/soa", json={"name": name}) - assert r.status_code == 200 - return r.json()["id"] - - -def _add_visit(soa_id, name, label=None): - payload = {"name": name, "label": label or name} - r = client.post(f"/soa/{soa_id}/visits", json=payload) - assert r.status_code == 200 - return r.json()["visit_id"] - - -def _add_activity(soa_id, name): - r = client.post(f"/soa/{soa_id}/activities", json={"name": name}) - assert r.status_code == 200 - return r.json()["activity_id"] - - -def _set_matrix_cell(soa_id, visit_id, activity_id, status="X"): - r = client.post( - f"/soa/{soa_id}/cells", - json={"visit_id": visit_id, "activity_id": activity_id, "status": status}, - ) - assert r.status_code == 200 - - -def test_delete_visit_cascades_and_reindexes(): - soa_id = _create_soa() - v1 = _add_visit(soa_id, "V1") - v2 = _add_visit(soa_id, "V2") - a1 = _add_activity(soa_id, "A1") - a2 = _add_activity(soa_id, "A2") - _set_matrix_cell(soa_id, v1, a1, "X") - _set_matrix_cell(soa_id, v2, a1, "X") - _set_matrix_cell(soa_id, v2, a2, "O") - - # initial matrix - m = client.get(f"/soa/{soa_id}/matrix").json() - assert len(m["visits"]) == 2 - assert len(m["activities"]) == 2 - assert len(m["cells"]) >= 3 # upserted matrix_cells present - - # delete first visit - dr = client.delete(f"/soa/{soa_id}/visits/{v1}") - assert dr.status_code == 200 - - m2 = client.get(f"/soa/{soa_id}/matrix").json() - assert len(m2["visits"]) == 1 - remaining_visit = m2["visits"][0] - # reindexed - assert remaining_visit["order_index"] == 1 - assert remaining_visit["name"] == "V2" - # matrix_cells referencing deleted visit removed - assert all(c["visit_id"] != v1 for c in m2["cells"]) - - # delete activity A1 - dr2 = client.delete(f"/soa/{soa_id}/activities/{a1}") - assert dr2.status_code == 200 - m3 = client.get(f"/soa/{soa_id}/matrix").json() - assert len(m3["activities"]) == 1 - remaining_activity = m3["activities"][0] - assert remaining_activity["order_index"] == 1 - assert remaining_activity["name"] == "A2" - assert all(c["activity_id"] != a1 for c in m3["cells"]) - - -def test_delete_activity_reindexes_only(): - soa_id = _create_soa("DelTest2") - v1 = _add_visit(soa_id, "Day1") - a1 = _add_activity(soa_id, "Draw") - a2 = _add_activity(soa_id, "Scan") - _set_matrix_cell(soa_id, v1, a1) - _set_matrix_cell(soa_id, v1, a2) - - m = client.get(f"/soa/{soa_id}/matrix").json() - assert [a["order_index"] for a in m["activities"]] == [1, 2] - - dr = client.delete(f"/soa/{soa_id}/activities/{a1}") - assert dr.status_code == 200 - m2 = client.get(f"/soa/{soa_id}/matrix").json() - assert len(m2["activities"]) == 1 - assert m2["activities"][0]["order_index"] == 1 - assert m2["activities"][0]["name"] == "Scan" - # matrix_cell referencing removed activity gone - assert all(c["activity_id"] != a1 for c in m2["cells"]) diff --git a/tests/test_exports.py b/tests/test_exports.py deleted file mode 100644 index 2996e41..0000000 --- a/tests/test_exports.py +++ /dev/null @@ -1,50 +0,0 @@ -from fastapi.testclient import TestClient - -from soa_builder.web.app import app - -client = TestClient(app) - - -def reset_db(): - # Disabled: preserve persistent DB across tests - return - - -def _setup_matrix(): - r = client.post("/soa", json={"name": "Export Trial"}) - soa_id = r.json()["id"] - v1 = client.post(f"/soa/{soa_id}/visits", json={"name": "C1D1"}).json()["visit_id"] - v2 = client.post(f"/soa/{soa_id}/visits", json={"name": "C1D8"}).json()["visit_id"] - a1 = client.post(f"/soa/{soa_id}/activities", json={"name": "Lab"}).json()[ - "activity_id" - ] - a2 = client.post(f"/soa/{soa_id}/activities", json={"name": "ECG"}).json()[ - "activity_id" - ] - client.post( - f"/soa/{soa_id}/cells", json={"visit_id": v1, "activity_id": a1, "status": "X"} - ) - client.post( - f"/soa/{soa_id}/cells", json={"visit_id": v2, "activity_id": a2, "status": "X"} - ) - return soa_id - - -def test_export_xlsx(): - reset_db() - soa_id = _setup_matrix() - resp = client.get(f"/soa/{soa_id}/export/xlsx") - assert resp.status_code == 200 - assert resp.headers["content-type"].startswith( - "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet" - ) - assert len(resp.content) > 1000 # basic size sanity - - -def test_export_pdf(): - reset_db() - soa_id = _setup_matrix() - resp = client.get(f"/soa/{soa_id}/export/pdf") - assert resp.status_code == 200 - assert resp.headers["content-type"] == "application/pdf" - assert len(resp.content) > 800 # PDF minimal bytes diff --git a/tests/test_ui_visit_create.py b/tests/test_ui_visit_create.py deleted file mode 100644 index a663521..0000000 --- a/tests/test_ui_visit_create.py +++ /dev/null @@ -1,64 +0,0 @@ -from fastapi.testclient import TestClient - -from soa_builder.web.app import _connect, app - -client = TestClient(app) - - -def _create_soa(name="UIVisitTest"): - resp = client.post("/soa", json={"name": name}) - assert resp.status_code == 200, resp.text - return resp.json()["id"] - - -def test_ui_add_visit_blank_epoch(): - soa_id = _create_soa() - # Post without epoch (form supplies blank) - resp = client.post( - f"/ui/soa/{soa_id}/add_visit", data={"name": "Visit 1", "label": ""} - ) - assert resp.status_code == 200, resp.text - # Fetch matrix to validate visit presence - m = client.get(f"/soa/{soa_id}/matrix") - assert m.status_code == 200 - data = m.json() - visits = data.get("visits") or [] - assert any( - v["name"] == "Visit 1" for v in visits - ), f"Visit not found in matrix: {visits}" - # Ensure epoch_id is null/None in DB - conn = _connect() - cur = conn.cursor() - cur.execute( - "SELECT epoch_id FROM visit WHERE soa_id=? AND name=?", (soa_id, "Visit 1") - ) - row = cur.fetchone() - conn.close() - assert row is not None - assert row[0] is None, f"Expected NULL epoch_id, got {row[0]}" - - -def test_ui_add_visit_with_epoch(): - soa_id = _create_soa("UIVisitEpochTest") - # Create an epoch first - resp_epoch = client.post(f"/ui/soa/{soa_id}/add_epoch", data={"name": "Screening"}) - assert resp_epoch.status_code == 200 - # Lookup epoch id - conn = _connect() - cur = conn.cursor() - cur.execute("SELECT id FROM epoch WHERE soa_id=? AND name=?", (soa_id, "Screening")) - eid = cur.fetchone()[0] - conn.close() - # Provide legacy field name epoch_id - resp = client.post( - f"/ui/soa/{soa_id}/add_visit", data={"name": "Visit A", "epoch_id": str(eid)} - ) - assert resp.status_code == 200, resp.text - m = client.get(f"/soa/{soa_id}/matrix") - data = m.json() - visits = data.get("visits") or [] - found = [v for v in visits if v["name"] == "Visit A"] - assert found, f"Visit A not found: {visits}" - assert ( - found[0]["epoch_id"] == eid - ), f"Expected epoch_id {eid}, got {found[0]['epoch_id']}" diff --git a/tests/test_web_api.py b/tests/test_web_api.py deleted file mode 100644 index 14eb0e1..0000000 --- a/tests/test_web_api.py +++ /dev/null @@ -1,46 +0,0 @@ -from fastapi.testclient import TestClient - -from soa_builder.web.app import app - -client = TestClient(app) - - -def reset_db(): - # Disabled: preserve persistent DB across tests - return - - -def test_create_and_normalize_flow(): - reset_db() - # create soa - r = client.post("/soa", json={"name": "Test Trial"}) - assert r.status_code == 200 - soa_id = r.json()["id"] - # add visit - rv = client.post( - f"/soa/{soa_id}/visits", - json={"name": "C1D1", "label": "Cycle 1 Day 1 (C1D1)"}, - ) - assert rv.status_code == 200 - visit_id = rv.json()["visit_id"] - # add activity - ra = client.post(f"/soa/{soa_id}/activities", json={"name": "Hematology"}) - assert ra.status_code == 200 - activity_id = ra.json()["activity_id"] - # set matrix_cell - rc = client.post( - f"/soa/{soa_id}/cells", - json={"visit_id": visit_id, "activity_id": activity_id, "status": "X"}, - ) - assert rc.status_code == 200 - # matrix - rm = client.get(f"/soa/{soa_id}/matrix") - assert rm.status_code == 200 - data = rm.json() - assert len(data["visits"]) == 1 and len(data["activities"]) == 1 - # normalized - rn = client.get(f"/soa/{soa_id}/normalized") - assert rn.status_code == 200 - summary = rn.json()["summary"] - assert summary["visits"] >= 1 - assert summary["activities"] >= 1 From b5f97940f0b37bd0052b3ef04aaecd23144dbbed Mon Sep 17 00:00:00 2001 From: Darren <3921919+pendingintent@users.noreply.github.com> Date: Thu, 8 Jan 2026 16:03:50 -0500 Subject: [PATCH 04/11] SOA MAtrix now uses ScheduledActivityInstance values as column headers for matrix --- src/soa_builder/web/app.py | 73 +++++++++++++++---- src/soa_builder/web/templates/edit.html | 31 +++++++- .../web/templates/freeze_modal.html | 39 ++++++++-- 3 files changed, 121 insertions(+), 22 deletions(-) diff --git a/src/soa_builder/web/app.py b/src/soa_builder/web/app.py index 450d23b..a287dba 100644 --- a/src/soa_builder/web/app.py +++ b/src/soa_builder/web/app.py @@ -632,17 +632,51 @@ def _diff_freezes_limited( } acts_added_all = [r_act[k] for k in r_act.keys() - l_act.keys()] acts_removed_all = [l_act[k] for k in l_act.keys() - r_act.keys()] - # Cells (status changes) - l_cells = { - (c["visit_id"], c["activity_id"]): c - for c in l_snap.get("cells", []) - if isinstance(c, dict) - } - r_cells = { - (c["visit_id"], c["activity_id"]): c - for c in r_snap.get("cells", []) - if isinstance(c, dict) - } + # Cells (status changes). Newer snapshots key by instance_id; older ones used visit_id. + + def _cell_key(cell: dict) -> Optional[tuple[str, int, int]]: + if not isinstance(cell, dict): + return None + activity_id = cell.get("activity_id") + if activity_id is None: + return None + if cell.get("instance_id") is not None: + return ("instance", int(cell["instance_id"]), int(activity_id)) + if cell.get("visit_id") is not None: + return ("visit", int(cell["visit_id"]), int(activity_id)) + return None + + def _normalize_cell(cell: dict) -> dict: + axis_type = ( + "instance" + if cell.get("instance_id") is not None + else "visit" if cell.get("visit_id") is not None else None + ) + axis_id = None + if axis_type == "instance": + axis_id = cell.get("instance_id") + elif axis_type == "visit": + axis_id = cell.get("visit_id") + return { + "axis_type": axis_type, + "axis_id": axis_id, + "instance_id": cell.get("instance_id"), + "visit_id": cell.get("visit_id"), + "activity_id": cell.get("activity_id"), + "status": cell.get("status"), + } + + def _build_cell_map(snapshot_cells: list[dict]) -> dict: + mapped = {} + for raw in snapshot_cells or []: + key = _cell_key(raw) + if not key: + continue + mapped[key] = _normalize_cell(raw) + return mapped + + l_cells = _build_cell_map(l_snap.get("cells", [])) + r_cells = _build_cell_map(r_snap.get("cells", [])) cells_added_all = [r_cells[k] for k in r_cells.keys() - l_cells.keys()] cells_removed_all = [l_cells[k] for k in l_cells.keys() - r_cells.keys()] cells_changed_all = [] @@ -650,8 +684,11 @@ def _diff_freezes_limited( if r_cells[k].get("status") != l_cells[k].get("status"): cells_changed_all.append( { - "visit_id": k[0], - "activity_id": k[1], + "axis_type": l_cells[k].get("axis_type"), + "axis_id": l_cells[k].get("axis_id"), + "visit_id": l_cells[k].get("visit_id"), + "instance_id": l_cells[k].get("instance_id"), + "activity_id": l_cells[k].get("activity_id"), "old_status": l_cells[k].get("status"), "new_status": r_cells[k].get("status"), } @@ -2005,7 +2042,11 @@ def _matrix_arrays(soa_id: int): """Return schedule instance headers list and rows (activity name + statuses).""" instances, activities, cells = _fetch_matrix(soa_id) instance_headers = [i["name"] for i in instances] - cell_lookup = {[c["instance_id"], c["activity_id"], c["status"]] for c in cells} + cell_lookup = { + (c["instance_id"], c["activity_id"]): c.get("status", "") + for c in cells + if c.get("instance_id") is not None and c.get("activity_id") is not None + } rows = [] for a in activities: row = [a["name"]] @@ -2543,7 +2584,7 @@ def export_xlsx(soa_id: int, left: Optional[int] = None, right: Optional[int] = visits, activities, cells = _fetch_matrix(soa_id) if not visits or not activities: raise HTTPException( - 400, "Cannot export empty matrix (need visits and activities)" + 400, "Cannot export empty matrix (need instances and activities)" ) headers, rows = _matrix_arrays(soa_id) # Build DataFrame, then inject Concepts column (second position) @@ -2694,7 +2735,7 @@ def export_xlsx(soa_id: int, left: Optional[int] = None, right: Optional[int] = ["Study Label", study_label_val or ""], ["Study Description", (study_desc_val or "")[:4000]], ["Created At", created_at_val or ""], - ["Visit Count", str(len(visits))], + ["Scheduled Activity Instances Count", str(len(visits))], ["Activity Count", str(len(activities))], ["Cell Count", str(cell_count)], ["Concept Mapping Count", str(concept_mapping_count)], diff --git a/src/soa_builder/web/templates/edit.html b/src/soa_builder/web/templates/edit.html index e5f8e2a..12bcb21 100644 --- a/src/soa_builder/web/templates/edit.html +++ b/src/soa_builder/web/templates/edit.html @@ -482,7 +482,13 @@

    Matrix

    Generate Normalized Summary (JSON)