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BICF
KCE
kce_etl
Commits
32e801e1
Commit
32e801e1
authored
Apr 28, 2020
by
Venkat Malladi
Browse files
Make lower case.
parent
cc57dc02
Pipeline
#6775
failed with stage
in 10 seconds
Changes
1
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
scripts/transform_medications.py
View file @
32e801e1
...
...
@@ -79,7 +79,7 @@ def filter_supp(supp_meds):
#Filter columns
supp_meds_reformated
=
meds_taken
[[
'MRN'
,
'Meds'
,
'START_DATE'
]]
supp_meds_reformated
.
columns
=
[
'mrn'
,
'name'
,
'
S
tart_date'
]
supp_meds_reformated
.
columns
=
[
'mrn'
,
'name'
,
'
s
tart_date'
]
return
supp_meds_reformated
,
meds_non_taken
...
...
@@ -170,22 +170,22 @@ def calculate_regime(meds):
# Format Oncological Meds
meds_filtered_uniq
=
meds_transformed
.
groupby
([
'mrn'
,
'name'
],
as_index
=
False
).
agg
({
'date'
:
[
np
.
min
,
np
.
max
],
'start'
:
[
np
.
min
],
'end'
:
[
np
.
max
]
})
meds_filtered_uniq
.
columns
=
[
'mrn'
,
'name'
,
'date_start'
,
'date_end'
,
'start'
,
'end'
]
meds_filtered_uniq
[
'
S
tart_date'
]
=
meds_filtered_uniq
[[
'date_start'
,
'date_end'
,
'start'
,
'end'
]].
min
(
axis
=
1
)
meds_filtered_uniq
[
'
E
nd_date'
]
=
meds_filtered_uniq
[[
'date_start'
,
'date_end'
,
'start'
,
'end'
]].
max
(
axis
=
1
)
meds_filtered_uniq
[
'Duration'
]
=
(
meds_filtered_uniq
[
'
E
nd_date'
]
-
meds_filtered_uniq
[
'
S
tart_date'
]).
dt
.
days
onco_meds_reformated
=
meds_filtered_uniq
[[
'mrn'
,
'name'
,
'
S
tart_date'
,
'
E
nd_date'
,
'Duration'
]]
meds_filtered_uniq
[
'
s
tart_date'
]
=
meds_filtered_uniq
[[
'date_start'
,
'date_end'
,
'start'
,
'end'
]].
min
(
axis
=
1
)
meds_filtered_uniq
[
'
e
nd_date'
]
=
meds_filtered_uniq
[[
'date_start'
,
'date_end'
,
'start'
,
'end'
]].
max
(
axis
=
1
)
meds_filtered_uniq
[
'Duration'
]
=
(
meds_filtered_uniq
[
'
e
nd_date'
]
-
meds_filtered_uniq
[
'
s
tart_date'
]).
dt
.
days
onco_meds_reformated
=
meds_filtered_uniq
[[
'mrn'
,
'name'
,
'
s
tart_date'
,
'
e
nd_date'
,
'Duration'
]]
# Reset duration for 0
onco_meds_reformated
.
loc
[
onco_meds_reformated
.
Duration
==
0
,
'
E
nd_date'
]
=
None
onco_meds_reformated
.
loc
[
onco_meds_reformated
.
Duration
==
0
,
'
e
nd_date'
]
=
None
onco_meds_reformated
.
loc
[
onco_meds_reformated
.
Duration
==
0
,
'Duration'
]
=
None
# If End Date > that current pull reset to null
onco_meds_reformated
.
loc
[
onco_meds_reformated
.
E
nd_date
>
datetime
.
datetime
(
2020
,
3
,
1
),
'
E
nd_date'
]
=
None
onco_meds_reformated
.
loc
[
onco_meds_reformated
.
E
nd_date
>
datetime
.
datetime
(
2020
,
3
,
1
),
'Duration'
]
=
None
onco_meds_reformated
.
loc
[
onco_meds_reformated
.
e
nd_date
>
datetime
.
datetime
(
2020
,
3
,
1
),
'
e
nd_date'
]
=
None
onco_meds_reformated
.
loc
[
onco_meds_reformated
.
e
nd_date
>
datetime
.
datetime
(
2020
,
3
,
1
),
'Duration'
]
=
None
# If End_date is null
onco_meds_reformated
.
loc
[
onco_meds_reformated
.
E
nd_date
.
isnull
(),
'
E
nd_date'
]
=
datetime
.
datetime
(
2020
,
3
,
1
)
onco_meds_reformated
[
'Duration'
]
=
(
onco_meds_reformated
[
'
E
nd_date'
]
-
onco_meds_reformated
[
'
S
tart_date'
]).
dt
.
days
onco_meds_reformated
.
loc
[
onco_meds_reformated
.
e
nd_date
.
isnull
(),
'
e
nd_date'
]
=
datetime
.
datetime
(
2020
,
3
,
1
)
onco_meds_reformated
[
'Duration'
]
=
(
onco_meds_reformated
[
'
e
nd_date'
]
-
onco_meds_reformated
[
'
s
tart_date'
]).
dt
.
days
onco_meds_reformated
=
onco_meds_reformated
.
reset_index
(
drop
=
True
)
...
...
@@ -197,17 +197,17 @@ def calculate_shift(meds, date_shift):
# Convert to DateTime
date_shift
[
'Shift'
]
=
pd
.
to_timedelta
(
date_shift
[
'Shift'
],
unit
=
's'
)
meds
[
'
S
tart_date'
]
=
pd
.
to_datetime
(
meds
[
'
S
tart_date'
])
meds
[
'
s
tart_date'
]
=
pd
.
to_datetime
(
meds
[
'
s
tart_date'
])
# Merge data
merged
=
meds
.
merge
(
date_shift
,
left_on
=
'mrn'
,
right_on
=
'MRN'
,
how
=
'inner'
)
# Calculate Date Shift
merged
[
'
S
tart_date'
]
=
merged
[
'
S
tart_date'
]
+
merged
[
'Shift'
]
merged
[
'
S
tart_date'
]
=
merged
[
'
S
tart_date'
].
dt
.
date
if
'
E
nd_date'
in
merged
.
columns
:
merged
[
'
E
nd_date'
]
=
merged
[
'
E
nd_date'
]
+
merged
[
'Shift'
]
merged
[
'
E
nd_date'
]
=
merged
[
'
E
nd_date'
].
dt
.
date
merged
[
'
s
tart_date'
]
=
merged
[
'
s
tart_date'
]
+
merged
[
'Shift'
]
merged
[
'
s
tart_date'
]
=
merged
[
'
s
tart_date'
].
dt
.
date
if
'
e
nd_date'
in
merged
.
columns
:
merged
[
'
e
nd_date'
]
=
merged
[
'
e
nd_date'
]
+
merged
[
'Shift'
]
merged
[
'
e
nd_date'
]
=
merged
[
'
e
nd_date'
].
dt
.
date
# Drop Shift column
merged
.
drop
([
'Shift'
],
axis
=
1
,
inplace
=
True
)
...
...
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