todo_wizard.yaml

  /wizard/todo:
    widget: !<Wizard>
      initial_context:
        individual: A00F5818
      states:
        todo:
          not-skipped-not-complete:
            title: Not Skipped
            expression: status!='skipped'&status!='complete'
          measure:
            title: Measure Todo
            expression: requirement.asset_type='measure'|measure_todo_fulfillment
          sample:
            title: Sample Todo
            expression: requirement.asset_type='sample'|sample_todo_fulfillment
          communication:
            title: Communication Todo
            expression: requirement.asset_type='communication'|communication_todo_fulfillment
          consent:
            title: Consent Todo
            expression: requirement.asset_type='consent'|consent_todo_fulfillment
          other:
            title: Other Todo
            expression: requirement.asset_type='consent'

          awaiting-measure:
            title: Measure Todo
            expression: (requirement.asset_type='measure'|measure_todo_fulfillment)&status!='skipped'&status!='complete'
          awaiting-sample:
            title: Sample Todo
            expression: (requirement.asset_type='sample'|sample_todo_fulfillment)&status!='skipped'&status!='complete'
          awaiting-communication:
            title: Communication Todo
            expression: (requirement.asset_type='communication'|communication_todo_fulfillment)&status!='skipped'&status!='complete'
          awaiting-consent:
            title: Consent Todo
            expression: (requirement.asset_type='consent'|consent_todo_fulfillment)&status!='skipped'&status!='complete'
          awaiting-other:
            title: Other Todo
            expression: requirement.asset_type='other'&status!='skipped'&status!='complete'

      path:
      - pick-todo:
        - view-todo:
        - proceed-measure-todo:
        - proceed-sample-todo:
          - view-sample:
          - edit-sample:
          - pick-tube:
            - view-tube:
            - edit-tube:
            - use-sample:
            - pick-tube-usage:
              - view-used-tube:
          - add-tube:
          - pick-used-tube:
            - view-used-tube:
        - proceed-communication-todo:
        - proceed-consent-todo:
        - proceed-other-todo:
        - skip-todo:
      - adhoc-measure-todo:
      - adhoc-consent-todo:
      - adhoc-sample-todo:
      actions:
        pick-todo:
          type: pick
          entity: todo
          title: Pick Todo
          input:
          - individual: individual
          mask: individual=$individual
          columns:
          - value_key: study_title
            type: calculation
            expression: study.title
            label: Study
          - value_key: time_period_title
            type: calculation
            expression: time_period.title
            label: Visit Name
          - value_key: expected_completion_date
            label: Expected Completion
          - value_key: title
            label: Title
          - value_key: status
            label: Status
        view-todo:
          type: view
          entity: todo
          title: Details
        skip-todo:
          type: skip-todo
          title: Skip Todo
          submit_to: !slot
            name: submit_to
            default: /htsql/skip_todo.htsql
          todo_details: !slot
            name: todo_details
            default: /data/individual/todo_details
          entity: todo[not-skipped-not-complete]
        proceed-measure-todo:
          type: proceed-measure-todo
          entity: todo[awaiting-measure]
          title: Fulfill Data Entry Todo
          data_entry_link: !slot
            name: data_entry_link
            default: rex.study.data_entry_admin:/data-entry
          reconciliation_link: !slot
            name: reconciliation_link
            default: rex.study.data_reconciliation_admin:/reconcile
          acquire_channel: !slot
            name: acquire_channel
            default: /data/acquire_channel
          measure_candidates: !slot
            name: measure_candidates
            default: /data/individual/todo_measure_candidates
          measure_types: !slot
            name: measure_types
            default: /data/individual/todo_measure_types
          measure_fulfillment: !slot
            name: measure_fulfillment
            default: /data/individual/todo_measure_fulfillment
          todo_details: !slot
            name: todo_details
            default: /data/individual/todo_details
          use_query: !slot
            name: use_query
            default: /htsql/use_existing_measure.htsql
          create_query: !slot
            name: use_query
            default: /htsql/create_new_measure.htsql
          clone_query: !slot
            name: clone_query
            default: /htsql/clone_existing_measure.htsql
        proceed-consent-todo:
          type: proceed-consent-todo
          entity: todo[awaiting-consent]
          title: Fulfill Consent Todo
          consent_types: !slot
            name: consent_types
            default: /data/individual/todo_consent_types
          create_query: !slot
            name: use_query
            default: /htsql/create_new_consent.htsql
          todo_details: !slot
            name: todo_details
            default: /data/individual/todo_details
          individual_data_spec: !slot
            name: individual_data_spec
            default: /data/individual/autocomplete
          consent_save: !slot
            name: consent_save
            default: /data/consent/save
          storage_link: !slot
            name: storage_link
            default: rex.file:/
          download_link: !slot
            name: download_link
            default: /data/consent/scan
        proceed-sample-todo:
          type: proceed-sample-todo
          entity: todo[awaiting-sample]
          title: Fulfill Sample Todo
          sample_types: !slot
            name: sample_types
            default: /data/individual/todo_sample_types
          create_query: !slot
            name: use_query
            default: /htsql/create_new_sample.htsql
          todo_details: !slot
            name: todo_details
            default: /data/individual/todo_details
          view_fields: !slot
            name: form_fields
            default:
            - value_key: sample_type
              label: Sample Type
            - value_key: individual
              label: Individual
            - value_key: code
              label: Code
            - value_key: code_text
              label: Code Text
            - value_key: date_collected
              label: Date Collected
            - value_key: collected_by
              label: Collected By
            - value_key: derived_from
              label: Derived From
          sample_details: !slot
            name: sample_details
            default: /data/individual/sample_details
        proceed-communication-todo:
          type: edit
          entity: todo[awaiting-communication]
          title: Fulfill Communication Todo
        proceed-other-todo:
          type: edit
          entity: todo[awaiting-other]
          title: Fulfill Other Todo

        #########################################
        ## Adhoc actions of TodoWizard:
        #########################################
        adhoc-measure-todo:
          type: make
          title: Add Measure Adhoc ToDo
          icon: plus
          entity: todo
          width: 700
          submit_button: Submit
          value:
            individual: $individual
            num_required_entries: '2'
            acquire_channel: entry
          fields:
          - value_key: study
            label: Study
            required: true
          - value_key: measure_type
            label: Measure Type
            type: entity
            required: true
            data:
              entity: measure_type
              title: title
          - value_key: expected_completion_date
            label: Expected Completion Date
            type: date
          - value_key: appointment_start
            label: Add Appointment Date
            type: datetime
          - value_key: appointment_type
            label: Appointment Type
            type: entity
            data:
              entity: appointment_type
              title: title
          - value_key: acquire_channel
            label: Acquire Channel
            type: entity
            required: true
            data:
              entity: acquire_channel
              title: title
          - value_key: num_required_entries
            pattern: '^\d+$'
            label: Number of required entries
            required: true
          query:
            /do(
              $_time_period := top(time_period.filter(study=$study&code='anytime')).id(),
              $_revision := max(
                  measure_type_revision.filter(
                    measure_type = $measure_type
                    & !is_null(json)
                    & exists(measure_type_revision_channel.acquire_channel = 'entry')
                    ).revision
              ),
              $_title := measure_type[$measure_type].title,
              $_measure := insert( measure :=
                    {
                        measure_type_revision := [[$measure_type].$_revision],
                        individual := [$individual],
                        study := [$study],
                        data_entry_status := 'in-process'
                    }
              ),
              $_appointment_type := if(is_null($appointment_type), 'home', $appointment_type),
              $_appointment := if (
                !is_null($appointment_start) & 
                !exists(appointment?individual=$individual
                        &appointment_type=$_appointment_type
                        &start=$appointment_start&(status='scheduled'|status='rescheduled')),
                insert( appointment := 
                {
                    individual := [$individual],
                    appointment_type := $_appointment_type,
                    start := $appointment_start,
                    duration := '1',
                    staff := [$USER],
                    requestor := [$USER],
                    acceptance_status_by_staff := 'requested',
                    status := 'scheduled'
                }),
                top(appointment?individual=$individual
                                   &appointment_type=$_appointment_type
                                   &start=$appointment_start).id()
              ),
              $_todo := insert( todo :=
                {
                    individual := [$individual],
                    study := [$study],
                    expected_completion_date := $expected_completion_date,
                    status := 'not-started',
                    title := $_title,
                    appointment := $_appointment,
                    time_period := $_time_period
                }
              ),
              $_measure_todo_fulfillment := insert( measure_todo_fulfillment :=
                {
                    todo := $_todo,
                    measure := $_measure,
                    num_required_entries := $num_required_entries,
                    acquire_channel := [$acquire_channel]
                }
              )
            )

        adhoc-consent-todo:
          type: make
          title: Add Consent Adhoc ToDo
          icon: plus
          width: 700
          entity: todo
          submit_button: Submit
          value:
            individual: $individual
          fields:
          - value_key: study
            label: Study
            required: true
          - type: entity
            label: Consent Type
            value_key: consent_type
            required: true
            data:
              entity: consent_type
              title: title
          - value_key: expected_completion_date
            label: Expected Completion Date
            type: date
          - value_key: appointment_start
            label: Appointment Date
            type: datetime
          - value_key: appointment_type
            label: Appointment Type
            type: entity
            data:
              entity: appointment_type
              title: title
          query:
            /do(
              $_time_period := top(time_period.filter(study=$study&code='anytime')).id(),
              $_title := consent_type[$consent_type].title,
              $_consent := insert( consent :=
                {
                    individual := [$individual],
                    consent_type := [$consent_type]
                }
              ),
              $_appointment_type := if(is_null($appointment_type), 'home', $appointment_type),
              $_appointment := if (
                !is_null($appointment_start) & 
                !exists(appointment?individual=$individual
                        &appointment_type=$_appointment_type
                        &(status='scheduled'|status='rescheduled')
                        &start=$appointment_start),
                insert( appointment := 
                {
                    individual := [$individual],
                    appointment_type := $_appointment_type,
                    start := $appointment_start,
                    duration := '1',
                    staff := [$USER],
                    requestor := [$USER],
                    acceptance_status_by_staff := 'requested',
                    status := 'scheduled'
                }),
                top(appointment?individual=$individual
                                   &appointment_type=$_appointment_type
                                   &start=$appointment_start).id()
              ),

              $_todo := insert( todo :=
                {
                    individual := [$individual],
                    study := [$study],
                    expected_completion_date := $expected_completion_date,
                    status := 'not-started',
                    title := $_title,
                    appointment := $_appointment,
                    time_period := $_time_period
                }
              ),
              $_consent_todo_fulfillment := insert( consent_todo_fulfillment :=
                {
                    todo := $_todo,
                    consent := $_consent
                }
              )
            )

        adhoc-sample-todo:
          type: make
          title: Add Sample Adhoc ToDo
          icon: plus
          width: 700
          entity: todo
          submit_button: Submit
          value:
            individual: $individual
          fields:
          - value_key: study
            label: Study
            required: true
          - type: entity
            label: Sample Type
            value_key: sample_type
            required: true
            data:
              entity: sample_type
              title: title
          - value_key: expected_completion_date
            label: Expected Completion Date
            type: date
          - value_key: appointment_start
            label: Appointment Date
            type: datetime
          - value_key: appointment_type
            label: Appointment Type
            type: entity
            data:
              entity: appointment_type
              title: title
          query:
            /do(
              $_time_period := top(time_period.filter(study=$study&code='anytime')).id(),
              $_title := sample_type[$sample_type].title,
              $_sample := insert( sample :=
                {
                    individual := [$individual],
                    sample_type := [$sample_type]
                }
              ),
              $_appointment_type := if(is_null($appointment_type), 'home', $appointment_type),
              $_appointment := if (
                !is_null($appointment_start) & 
                !exists(appointment?individual=$individual
                        &appointment_type=$_appointment_type
                        &(status='scheduled'|status='rescheduled')
                        &start=$appointment_start),
                insert( appointment := 
                {
                    individual := [$individual],
                    appointment_type := $_appointment_type,
                    start := $appointment_start,
                    duration := '1',
                    staff := [$USER],
                    requestor := [$USER],
                    acceptance_status_by_staff := 'requested',
                    status := 'scheduled'
                }),
                top(appointment?individual=$individual
                                   &appointment_type=$_appointment_type
                                   &start=$appointment_start).id()
              ),

              $_todo := insert( todo :=
                {
                    individual := [$individual],
                    study := [$study],
                    expected_completion_date := $expected_completion_date,
                    status := 'not-started',
                    title := $_title,
                    appointment := $_appointment,
                    time_period := $_time_period
                }
              ),
              $_sample_todo_fulfillment := insert( sample_todo_fulfillment :=
                {
                    todo := $_todo,
                    sample := $_sample
                }
              )
            )

        #########################################
        ##  Sample actions of TodoWizard:
        #########################################
        edit-tube:
          type: edit
          entity: tube
          width: 500
          submit_button: Submit
          input:
          - tube: tube
          fields:
          - value_key: volume_amount
            label: Volume Amount
            required: true
            type: number
          - value_key: volume_unit
            label: Volume Unit
            required: true
          - value_key: concentration_amount
            label:  Concentration Amount
            required: true
            type: number
          - value_key: concentration_unit
            label: Concentration Unit
            required: true
          - value_key: location_memo
            label: Location Memo
            type: note
        view-sample:
          title: View
          type: view
          width: 500
          entity: sample
          input:
          - sample: sample
          fields:
          - value_key: code_text
            label: Sample Code
          - value_key: sample_type
            label: Sample Type
            type: calculation
            expression: sample_type.title
          - value_key: derived_from
            label: Derived From
            type: calculation
            expression: (derived_from.sample_type.title + ' - '+ derived_from.code_text)
          - value_key: remaining_volume_ml
            type: calculation
            label: Remaining Volume
            expression: if(exists(tube), str(sum(tube.volume_amount * switch(tube.volume_unit,
                                                       null(), 1,
                                                       'ml',   1,
                                                       'ul',   0.001)) -
                        sum(tube.tube_usage.used_volume_amount * switch(tube.tube_usage.used_volume_unit,
                                                        null(), 1,
                                                        'ml',   1,
                                                        'ul',   0.001))) + ' (ml)', '')
        pick-tube:
          type: pick
          title: Sample Tubes
          entity: tube
          width: 700
          input:
          - sample: sample
          mask: sample=$sample
          fields:
          - value_key: code
            label: Code
            width: 100
          - value_key: volume_amount
            width: 100
            label: Volume
          - value_key: volume_unit
            width: 100
            label: Unit
          - value_key: concentration_amount
            label: Concentration
          - value_key: concentration_unit
            label: Unit
          - value_key: remaining_volume_ml
            type: calculation
            label: Remaining Vol.
            expression: |
               switch(volume_unit, 
                       null(), volume_amount - sum(
                           if(tube_usage.used_volume_unit = 'ul', 
                              tube_usage.used_volume_amount*0.001,
                              tube_usage.used_volume_amount)),
                       'ml', volume_amount - sum(
                           if(tube_usage.used_volume_unit = 'ul', 
                              tube_usage.used_volume_amount*0.001,
                              tube_usage.used_volume_amount)),
                       'ul', volume_amount - sum(
                           if(tube_usage.used_volume_unit = 'ml'|is_null(tube_usage.used_volume_unit),
                              tube_usage.used_volume_amount*1000,
                              tube_usage.used_volume_amount)))
        view-tube:
          title: View Tube
          type: view
          width: 500
          entity: tube
          input:
          - tube: tube
          fields:
          - value_key: sample
            label: Sample
          - value_key: code
            label: Tube Code
          - value_key: volume_amount
            label: Volume
          - value_key: volume_unit
            label: Unit
          - value_key: concentration_amount
            label: Concentration
          - value_key: concentration_unit
            label: Unit
          - value_key: remaining_volume_ml
            type: calculation
            label: Remaining Volume
            expression: |
               str(switch(volume_unit, 
                       null(), volume_amount - sum(
                           if(tube_usage.used_volume_unit = 'ul', 
                              tube_usage.used_volume_amount*0.001,
                              tube_usage.used_volume_amount)),
                       'ml', volume_amount - sum(
                           if(tube_usage.used_volume_unit = 'ul', 
                              tube_usage.used_volume_amount*0.001,
                              tube_usage.used_volume_amount)),
                       'ul', volume_amount - sum(
                           if(tube_usage.used_volume_unit = 'ml'|is_null(tube_usage.used_volume_unit),
                              tube_usage.used_volume_amount*1000,
                              tube_usage.used_volume_amount)))) + ' (' + str(volume_unit) + ')'

          - value_key: location_memo
            label: Location
        use-sample:
          type: make
          title: Use Sample
          entity: tube_usage
          width: 500
          submit_button: Submit
          value:
            tube: $tube
          fields:
          - value_key: tube
            label: Tube
            read_only: true
            type: entity
            data:
              entity: tube
              title: |
                (code + ' (' + str(switch(volume_unit, 
                       null(), volume_amount - sum(
                           if(tube_usage.used_volume_unit = 'ul', 
                              tube_usage.used_volume_amount*0.001,
                              tube_usage.used_volume_amount)),
                       'ml', volume_amount - sum(
                           if(tube_usage.used_volume_unit = 'ul', 
                              tube_usage.used_volume_amount*0.001,
                              tube_usage.used_volume_amount)),
                       'ul', volume_amount - sum(
                           if(tube_usage.used_volume_unit = 'ml'|is_null(tube_usage.used_volume_unit),
                              tube_usage.used_volume_amount*1000,
                              tube_usage.used_volume_amount)))) + ' ' + str(volume_unit) + ' remaining)')
          - value_key: used_volume_amount
            label: Volume Used
            required: true
          - value_key: used_volume_unit
            label: Volume Unit
            required: true
          - value_key: user
            label: Requested By
            type: entity
            data:
              entity: user
              title: remote_user
            required: true
          - value_key: date_requested
            label: Requested On
          - value_key: note
            label: Usage Note
            type: note
        edit-sample:
          title: Edit Sample
          type: edit
          entity: sample
          width: 500
          submit_button: Complete
          input:
          - sample: sample
          fields:
          - value_key: code_text
            label: Code
            required: true
          - value_key: sample_type
            label: Type
            required: true
          - value_key: derived_from
            label: Derived From
            type: entity
            data:
              entity: sample
              title: (sample_type.title + ' - '+ code_text)
        add-tube:
          type: make
          title: Add Tube
          entity: tube
          width: 600
          value:
            sample: $sample
          input:
          - sample: sample
          fields:
          - value_key: volume_amount
            label: Volume Amount
            required: true
          - value_key: volume_unit
            label: Volume Unit
            required: true
          - value_key: concentration_amount
            label:  Concentration Amount
            required: true
          - value_key: concentration_unit
            label: Concentration Unit
            required: true
          - value_key: location_memo
            label: Location Memo
            type: note
        pick-used-tube:
          type: pick
          title: Tubes Usage
          entity: tube_usage
          input:
          - sample: sample
          mask: tube.sample=$sample
          fields:
          - value_key: code
            label: Tube
          - value_key: used_volume_amount
            label: Used Vol. Amount
          - value_key: used_volume_unit
            label: Used Vol. Unit
          - value_key: date_requested
            label: Requested On
        view-used-tube:
          type: view
          title: View
          entity: tube_usage
          input:
          - tube_usage: tube_usage
          fields:
          - value_key: sample
            label: Sample
            type: calculation
            expression: tube.sample.id()
          - value_key: code
            label: Tube
          - value_key: user
            label: Requested By
          - value_key: used_volume_amount
            label: Used Volume Amount
          - value_key: used_volume_unit
            label: Used Volume Unit
          - value_key: date_requested
            label: Requested On
          - value_key: note
            label: Usage Note
        pick-tube-usage:
          type: pick
          title: Tube Usage
          entity: tube_usage
          input:
          - tube: tube
          mask: tube=$tube
          fields:
          - value_key: code
            label: Tube
          - value_key: used_volume_amount
            label: Used Vol. Amount
          - value_key: used_volume_unit
            label: Used Vol. Unit
          - value_key: date_requested
            label: Requested On