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vidjil
vidjil
Commits
4b7c3f73
Commit
4b7c3f73
authored
Oct 08, 2020
by
marc duez
Browse files
migrator.py : set obsolete key to default value
parent
244b26a2
Changes
1
Hide whitespace changes
Inline
Side-by-side
server/web2py/applications/vidjil/scripts/migrator.py
View file @
4b7c3f73
...
...
@@ -136,7 +136,8 @@ class Extractor():
memberships
=
{}
sequence_files
=
{}
for
row
in
rows
:
row
.
provider
=
1
row
.
sequence_file
.
provider
=
1
row
.
sequence_file
.
patient_id
=
None
ssm_id
=
row
.
sample_set_membership
.
id
sf_id
=
row
.
sequence_file
.
id
self
.
log
.
debug
(
"populating sequence file: %d, membership: %d"
%
(
sf_id
,
ssm_id
))
...
...
@@ -343,7 +344,12 @@ def import_data(filesrc, filedest, groupid, config=None, dry_run=False, log=Migr
if
stype
in
data
:
imp
.
importSampleSets
(
stype
,
data
[
stype
])
imp
.
importTable
(
'sequence_file'
,
data
[
'sequence_file'
],
map_val
=
True
)
for
row
in
data
[
'analysis_file'
]:
data
[
'analysis_file'
][
row
][
'patient_id'
]
=
None
data
[
'analysis_file'
][
row
][
'config_id'
]
=
None
for
row
in
data
[
'fused_file'
]:
data
[
'fused_file'
][
row
][
'patient_id'
]
=
None
imp
.
importTable
(
'sample_set_membership'
,
data
[
'membership'
],
{
'sample_set'
:
'sample_set_id'
,
'sequence_file'
:
'sequence_file_id'
})
imp
.
importTable
(
'scheduler_task'
,
data
[
'scheduler_task'
],
map_val
=
True
)
imp
.
importTable
(
'scheduler_run'
,
data
[
'scheduler_run'
],
{
'scheduler_task'
:
'task_id'
})
...
...
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