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Consulta PIVOT em registros distintos


Se você adicionar um ROW_NUMBER() ao mix, seu pivô poderá reter a associação entre atividades e porcentagens.
;with cte as 
(
    select *, ROW_NUMBER() over (partition by name order by percentage desc) ROWNUM
    from A
),
cte2 as
(
    SELECT Id,Code,ROWNUM,James,James_,Sam,Sam_,Lisa,Lisa_
    FROM cte
    PIVOT(MAX(activity)
          FOR name IN (James,Sam,Lisa)) AS PVTTable PIVOT
          (
          MAX(percentage)
          FOR name1 IN (James_,Sam_,Lisa_)) AS PVTTable1
)
select Id, Code, MAX(James) James, MAX(James_) James_, MAX(Sam) Sam, MAX(Sam_) Sam_, MAX(Lisa) Lisa, MAX(Lisa_) Lisa_
from cte2
group by Id, Code, ROWNUM

Devoluções:
Id  Code        James       James_  Sam         Sam_    Lisa    Lisa_
1   Prashant    Running     43.43   Cooking 1   73      Walking 90.34
1   Prashant    Stealing    0.00    Cooking     3.43    NULL    NULL
1   Prashant    Lacking     0.00    NULL        NULL    NULL    NULL

A ideia é, na primeira expressão de tabela comum, você transformar a tabela A para isso:
Id  Code        percentage  name    name1   activity    ROWNUM
1   Prashant    43.43       James   James_  Running     1
1   Prashant    0.00        James   James_  Stealing    2
1   Prashant    0.00        James   James_  Lacking     3
1   Prashant    90.34       Lisa    Lisa_   Walking     1
1   Prashant    73          Sam     Sam_    Cooking 1   1
1   Prashant    3.43        Sam     Sam_    Cooking     2

E em toda a consulta restante, a coluna ROWNUM apenas atua para vincular o valor percentual à atividade.

Torná-lo dinâmico é fácil quando você tem uma consulta em funcionamento. Basta substituir todas as partes dinâmicas (neste caso, listas de nomes delimitadas por vírgulas, certo?) por variáveis. Algo assim:
declare @sql nvarchar(max)
declare @name_concat nvarchar(max)
declare @name1_concat nvarchar(max)
declare @select_aggs nvarchar(max)
select @name_concat = STUFF((select distinct ',' + quotename(name) from A order by 1 for xml path('')), 1, 1, '')
select @name1_concat = STUFF((select distinct ',' + quotename(name1) from A order by 1 for xml path('')), 1, 1, '')

;with cte_all_names as (
    select name from A
    union all 
    select name1 from A
)
select @select_aggs = STUFF((select distinct ',MAX(' + quotename(name) + ') ' + quotename(name) from cte_all_names order by 1 for xml path('')), 1, 1, '')

select @sql = '
;with cte as 
(
    select *, ROW_NUMBER() over (partition by name order by percentage desc) ROWNUM
    from A
),
cte2 as
(
    SELECT Id,Code,ROWNUM,' + @name_concat + ',' + @name1_concat + '
    FROM cte
    PIVOT(MAX(activity)
          FOR name IN (' + @name_concat + ')) AS PVTTable PIVOT
          (
          MAX(percentage)
          FOR name1 IN (' + @name1_concat + ')) AS PVTTable1
)
select Id, Code, ' + @select_aggs + '
from cte2
group by Id, Code, ROWNUM
'

exec sp_executesql @sql