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SMASCH
scheduling-system
Commits
b4967fca
Commit
b4967fca
authored
4 years ago
by
Piotr Gawron
Browse files
Options
Downloads
Patches
Plain Diff
virus data are filled in loop instead of copy paste
parent
75cb53ff
No related branches found
No related tags found
1 merge request
!253
Resolve "import of serology data"
Changes
1
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1 changed file
smash/web/api_views/subject.py
+28
-44
28 additions, 44 deletions
smash/web/api_views/subject.py
with
28 additions
and
44 deletions
smash/web/api_views/subject.py
+
28
−
44
View file @
b4967fca
import
logging
import
logging
import
re
import
re
from
django.db.models
import
Count
,
Case
,
When
,
Min
,
Max
from
django.db.models
import
Count
,
Case
,
When
,
Min
,
Max
from
django.db.models
import
Q
from
django.db.models
import
Q
from
django.http
import
JsonResponse
from
django.http
import
JsonResponse
...
@@ -90,8 +91,8 @@ def get_subject_columns(request, subject_list_type):
...
@@ -90,8 +91,8 @@ def get_subject_columns(request, subject_list_type):
visit_numbers
=
range
(
1
,
study
.
visits_to_show_in_subject_list
+
1
)
visit_numbers
=
range
(
1
,
study
.
visits_to_show_in_subject_list
+
1
)
for
one_based_idx
,
virus_visit_number
in
enumerate
(
virus_visit_numbers
,
1
):
for
one_based_idx
,
virus_visit_number
in
enumerate
(
virus_visit_numbers
,
1
):
add_column
(
result
,
add_column
(
result
,
'
Virus {} RT-PCR
'
.
format
(
virus_visit_number
),
'
Virus {} RT-PCR
'
.
format
(
virus_visit_number
),
'
virus_test_{}
'
.
format
(
one_based_idx
),
#always starts in 1
'
virus_test_{}
'
.
format
(
one_based_idx
),
#always starts in 1
study_subject_columns
,
study_subject_columns
,
'
yes_no_null_inconclusive_filter
'
,
study
.
columns
)
'
yes_no_null_inconclusive_filter
'
,
study
.
columns
)
...
@@ -118,10 +119,10 @@ def get_subject_columns(request, subject_list_type):
...
@@ -118,10 +119,10 @@ def get_subject_columns(request, subject_list_type):
add_column
(
result
,
"
Type
"
,
"
type
"
,
study_subject_columns
,
"
type_filter
"
,
study
.
columns
)
add_column
(
result
,
"
Type
"
,
"
type
"
,
study_subject_columns
,
"
type_filter
"
,
study
.
columns
)
add_column
(
result
,
"
Edit
"
,
"
edit
"
,
None
,
None
,
sortable
=
False
)
add_column
(
result
,
"
Edit
"
,
"
edit
"
,
None
,
None
,
sortable
=
False
)
for
one_based_idx
,
visit_number
in
enumerate
(
visit_numbers
,
1
):
for
one_based_idx
,
visit_number
in
enumerate
(
visit_numbers
,
1
):
visit_key
=
"
visit_{}
"
.
format
(
one_based_idx
)
#always starts in 1
visit_key
=
"
visit_{}
"
.
format
(
one_based_idx
)
#always starts in 1
add_column
(
result
,
"
Visit {}
"
.
format
(
visit_number
),
visit_key
,
None
,
add_column
(
result
,
"
Visit {}
"
.
format
(
visit_number
),
visit_key
,
None
,
"
visit_filter
"
,
visible_param
=
study_subject_list
.
visits
)
"
visit_filter
"
,
visible_param
=
study_subject_list
.
visits
)
return
JsonResponse
({
"
columns
"
:
result
})
return
JsonResponse
({
"
columns
"
:
result
})
...
@@ -215,15 +216,15 @@ def get_subjects_order(subjects_to_be_ordered, order_column, order_direction, co
...
@@ -215,15 +216,15 @@ def get_subjects_order(subjects_to_be_ordered, order_column, order_direction, co
elif
str
(
order_column
).
startswith
(
"
visit_
"
):
elif
str
(
order_column
).
startswith
(
"
visit_
"
):
visit_number
=
get_visit_number_from_visit_x_string
(
order_column
)
visit_number
=
get_visit_number_from_visit_x_string
(
order_column
)
result
=
order_by_visit
(
subjects_to_be_ordered
,
order_direction
,
visit_number
)
result
=
order_by_visit
(
subjects_to_be_ordered
,
order_direction
,
visit_number
)
elif
re
.
search
(
r
'
^virus_test_[1-5]$
'
,
order_column
):
elif
re
.
search
(
r
'
^virus_test_[1-5]$
'
,
order_column
):
result
=
subjects_to_be_ordered
.
order_by
(
order_direction
+
order_column
)
result
=
subjects_to_be_ordered
.
order_by
(
order_direction
+
order_column
)
elif
re
.
search
(
r
'
^virus_test_[1-5]_updated$
'
,
order_column
):
elif
re
.
search
(
r
'
^virus_test_[1-5]_updated$
'
,
order_column
):
result
=
subjects_to_be_ordered
.
order_by
(
order_direction
+
order_column
)
result
=
subjects_to_be_ordered
.
order_by
(
order_direction
+
order_column
)
elif
re
.
search
(
r
'
^virus_test_[1-5]_collection_date
'
,
order_column
):
elif
re
.
search
(
r
'
^virus_test_[1-5]_collection_date
'
,
order_column
):
result
=
subjects_to_be_ordered
.
order_by
(
order_direction
+
order_column
)
result
=
subjects_to_be_ordered
.
order_by
(
order_direction
+
order_column
)
elif
re
.
search
(
r
'
^virus_test_[1-5]_iga_status
'
,
order_column
):
elif
re
.
search
(
r
'
^virus_test_[1-5]_iga_status
'
,
order_column
):
result
=
subjects_to_be_ordered
.
order_by
(
order_direction
+
order_column
)
result
=
subjects_to_be_ordered
.
order_by
(
order_direction
+
order_column
)
elif
re
.
search
(
r
'
^virus_test_[1-5]_igg_status
'
,
order_column
):
elif
re
.
search
(
r
'
^virus_test_[1-5]_igg_status
'
,
order_column
):
result
=
subjects_to_be_ordered
.
order_by
(
order_direction
+
order_column
)
result
=
subjects_to_be_ordered
.
order_by
(
order_direction
+
order_column
)
else
:
else
:
logger
.
warn
(
"
Unknown sort column:
"
+
str
(
order_column
))
logger
.
warn
(
"
Unknown sort column:
"
+
str
(
order_column
))
...
@@ -360,25 +361,25 @@ def get_subjects_filtered(subjects_to_be_filtered, filters):
...
@@ -360,25 +361,25 @@ def get_subjects_filtered(subjects_to_be_filtered, filters):
else
:
else
:
result
=
result
.
filter
(
virus_test_5
=
(
value
==
"
true
"
))
result
=
result
.
filter
(
virus_test_5
=
(
value
==
"
true
"
))
elif
column
==
"
virus_test_1_iga_status
"
:
elif
column
==
"
virus_test_1_iga_status
"
:
result
=
result
.
filter
(
virus_test_1_iga_status
=
value
)
result
=
result
.
filter
(
virus_test_1_iga_status
=
value
)
elif
column
==
"
virus_test_1_igg_status
"
:
elif
column
==
"
virus_test_1_igg_status
"
:
result
=
result
.
filter
(
virus_test_1_igg_status
=
value
)
result
=
result
.
filter
(
virus_test_1_igg_status
=
value
)
elif
column
==
"
virus_test_2_iga_status
"
:
elif
column
==
"
virus_test_2_iga_status
"
:
result
=
result
.
filter
(
virus_test_2_iga_status
=
value
)
result
=
result
.
filter
(
virus_test_2_iga_status
=
value
)
elif
column
==
"
virus_test_2_igg_status
"
:
elif
column
==
"
virus_test_2_igg_status
"
:
result
=
result
.
filter
(
virus_test_2_igg_status
=
value
)
result
=
result
.
filter
(
virus_test_2_igg_status
=
value
)
elif
column
==
"
virus_test_3_iga_status
"
:
elif
column
==
"
virus_test_3_iga_status
"
:
result
=
result
.
filter
(
virus_test_3_iga_status
=
value
)
result
=
result
.
filter
(
virus_test_3_iga_status
=
value
)
elif
column
==
"
virus_test_3_igg_status
"
:
elif
column
==
"
virus_test_3_igg_status
"
:
result
=
result
.
filter
(
virus_test_3_igg_status
=
value
)
result
=
result
.
filter
(
virus_test_3_igg_status
=
value
)
elif
column
==
"
virus_test_4_iga_status
"
:
elif
column
==
"
virus_test_4_iga_status
"
:
result
=
result
.
filter
(
virus_test_4_iga_status
=
value
)
result
=
result
.
filter
(
virus_test_4_iga_status
=
value
)
elif
column
==
"
virus_test_4_igg_status
"
:
elif
column
==
"
virus_test_4_igg_status
"
:
result
=
result
.
filter
(
virus_test_4_igg_status
=
value
)
result
=
result
.
filter
(
virus_test_4_igg_status
=
value
)
elif
column
==
"
virus_test_5_iga_status
"
:
elif
column
==
"
virus_test_5_iga_status
"
:
result
=
result
.
filter
(
virus_test_5_iga_status
=
value
)
result
=
result
.
filter
(
virus_test_5_iga_status
=
value
)
elif
column
==
"
virus_test_5_igg_status
"
:
elif
column
==
"
virus_test_5_igg_status
"
:
result
=
result
.
filter
(
virus_test_5_igg_status
=
value
)
result
=
result
.
filter
(
virus_test_5_igg_status
=
value
)
elif
column
==
"
brain_donation_agreement
"
:
elif
column
==
"
brain_donation_agreement
"
:
result
=
result
.
filter
(
brain_donation_agreement
=
(
value
==
"
true
"
))
result
=
result
.
filter
(
brain_donation_agreement
=
(
value
==
"
true
"
))
elif
column
==
"
postponed
"
:
elif
column
==
"
postponed
"
:
...
@@ -544,31 +545,6 @@ def serialize_subject(study_subject):
...
@@ -544,31 +545,6 @@ def serialize_subject(study_subject):
"
dead
"
:
bool_to_yes_no
(
study_subject
.
subject
.
dead
),
"
dead
"
:
bool_to_yes_no
(
study_subject
.
subject
.
dead
),
"
resigned
"
:
bool_to_yes_no
(
study_subject
.
resigned
),
"
resigned
"
:
bool_to_yes_no
(
study_subject
.
resigned
),
"
endpoint_reached
"
:
bool_to_yes_no
(
study_subject
.
endpoint_reached
),
"
endpoint_reached
"
:
bool_to_yes_no
(
study_subject
.
endpoint_reached
),
"
virus_test_1
"
:
virus_test_to_str
(
study_subject
.
virus_test_1
,
study_subject
.
virus_test_1_updated
),
"
virus_test_2
"
:
virus_test_to_str
(
study_subject
.
virus_test_2
,
study_subject
.
virus_test_2_updated
),
"
virus_test_3
"
:
virus_test_to_str
(
study_subject
.
virus_test_3
,
study_subject
.
virus_test_3_updated
),
"
virus_test_4
"
:
virus_test_to_str
(
study_subject
.
virus_test_4
,
study_subject
.
virus_test_4_updated
),
"
virus_test_5
"
:
virus_test_to_str
(
study_subject
.
virus_test_5
,
study_subject
.
virus_test_5_updated
),
"
virus_test_1_updated
"
:
study_subject
.
virus_test_1_updated
,
"
virus_test_2_updated
"
:
study_subject
.
virus_test_2_updated
,
"
virus_test_3_updated
"
:
study_subject
.
virus_test_3_updated
,
"
virus_test_4_updated
"
:
study_subject
.
virus_test_4_updated
,
"
virus_test_5_updated
"
:
study_subject
.
virus_test_5_updated
,
"
virus_test_1_collection_date
"
:
study_subject
.
virus_test_1_collection_date
,
"
virus_test_2_collection_date
"
:
study_subject
.
virus_test_2_collection_date
,
"
virus_test_3_collection_date
"
:
study_subject
.
virus_test_3_collection_date
,
"
virus_test_4_collection_date
"
:
study_subject
.
virus_test_4_collection_date
,
"
virus_test_5_collection_date
"
:
study_subject
.
virus_test_5_collection_date
,
"
virus_test_1_iga_status
"
:
study_subject
.
virus_test_1_iga_status
,
"
virus_test_1_igg_status
"
:
study_subject
.
virus_test_1_igg_status
,
"
virus_test_2_iga_status
"
:
study_subject
.
virus_test_2_iga_status
,
"
virus_test_2_igg_status
"
:
study_subject
.
virus_test_2_igg_status
,
"
virus_test_3_iga_status
"
:
study_subject
.
virus_test_3_iga_status
,
"
virus_test_3_igg_status
"
:
study_subject
.
virus_test_3_igg_status
,
"
virus_test_4_iga_status
"
:
study_subject
.
virus_test_4_iga_status
,
"
virus_test_4_igg_status
"
:
study_subject
.
virus_test_4_igg_status
,
"
virus_test_5_iga_status
"
:
study_subject
.
virus_test_5_iga_status
,
"
virus_test_5_igg_status
"
:
study_subject
.
virus_test_5_igg_status
,
"
postponed
"
:
bool_to_yes_no
(
study_subject
.
postponed
),
"
postponed
"
:
bool_to_yes_no
(
study_subject
.
postponed
),
"
brain_donation_agreement
"
:
bool_to_yes_no
(
study_subject
.
brain_donation_agreement
),
"
brain_donation_agreement
"
:
bool_to_yes_no
(
study_subject
.
brain_donation_agreement
),
"
excluded
"
:
bool_to_yes_no
(
study_subject
.
excluded
),
"
excluded
"
:
bool_to_yes_no
(
study_subject
.
excluded
),
...
@@ -580,4 +556,12 @@ def serialize_subject(study_subject):
...
@@ -580,4 +556,12 @@ def serialize_subject(study_subject):
"
id
"
:
study_subject
.
id
,
"
id
"
:
study_subject
.
id
,
"
visits
"
:
serialized_visits
,
"
visits
"
:
serialized_visits
,
}
}
for
i
in
range
(
1
,
6
):
result
[
'
virus_test_{}
'
.
format
(
i
)]
=
virus_test_to_str
(
getattr
(
study_subject
,
"
virus_test_{}
"
.
format
(
i
)),
getattr
(
study_subject
,
"
virus_test_{}_updated
"
.
format
(
i
)))
result
[
"
virus_test_{}_updated
"
.
format
(
i
)]
=
getattr
(
study_subject
,
"
virus_test_{}_updated
"
.
format
(
i
))
result
[
"
virus_test_{}_collection_date
"
.
format
(
i
)]
=
getattr
(
study_subject
,
"
virus_test_{}_collection_date
"
.
format
(
i
))
result
[
"
virus_test_{}_iga_status
"
.
format
(
i
)]
=
getattr
(
study_subject
,
"
virus_test_{}_iga_status
"
.
format
(
i
))
result
[
"
virus_test_{}_igg_status
"
.
format
(
i
)]
=
getattr
(
study_subject
,
"
virus_test_{}_igg_status
"
.
format
(
i
))
return
result
return
result
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