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vidjil
vidjil
Commits
58932022
Commit
58932022
authored
Oct 09, 2020
by
marc duez
Browse files
Merge branch 'feature-s/fix_migrator_script' into 'dev'
Feature s/fix migrator script See merge request
!818
parents
e9393969
de12acb3
Pipeline
#175995
passed with stages
in 14 minutes and 42 seconds
Changes
1
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
server/web2py/applications/vidjil/scripts/migrator.py
View file @
58932022
...
...
@@ -247,8 +247,11 @@ def copy_files(data, src, dest, log=MigrateLogger()):
for
t
in
file_fields
:
for
entry
in
data
[
t
]:
if
(
data
[
t
][
entry
][
file_fields
[
t
]]
is
not
None
):
log
.
debug
(
"Copying %s"
%
data
[
t
][
entry
][
file_fields
[
t
]])
copy
(
src
+
'/'
+
data
[
t
][
entry
][
file_fields
[
t
]],
dest
+
'/'
+
data
[
t
][
entry
][
file_fields
[
t
]])
try
:
copy
(
src
+
'/'
+
data
[
t
][
entry
][
file_fields
[
t
]],
dest
+
'/'
+
data
[
t
][
entry
][
file_fields
[
t
]])
log
.
debug
(
"Copying %s"
%
data
[
t
][
entry
][
file_fields
[
t
]])
except
:
log
.
error
(
"failed to copy file %s"
%
data
[
t
][
entry
][
file_fields
[
t
]])
def
export_peripheral_data
(
extractor
,
data_dict
,
sample_set_ids
,
log
=
MigrateLogger
()):
sequence_rows
=
extractor
.
getSequenceFiles
(
sample_set_ids
)
...
...
@@ -369,9 +372,9 @@ def import_data(filesrc, filedest, groupid, config=None, pprocess=None, dry_run=
db
.
rollback
()
log
.
info
(
"dry run successful, no data saved"
)
else
:
db
.
commit
()
log
.
info
(
"copying files from %s to %s"
%
(
filesrc
,
filedest
))
copy_files
(
data
,
filesrc
+
'/files'
,
filedest
,
log
=
log
)
db
.
commit
()
log
.
info
(
"done"
)
except
:
log
.
error
(
"something went wrong, rolling back"
)
...
...
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