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abims
e-infra
gga_load_data
Commits
59992b00
Commit
59992b00
authored
3 years ago
by
Loraine Gueguen
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fix run_tool call
parent
ea09cb2e
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2 merge requests
!12
Release_2.0 next
,
!9
Release 2.0 (merge dev to master)
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gga_load_data.py
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1
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59992b00
...
@@ -69,7 +69,8 @@ class LoadData(speciesData.SpeciesData):
...
@@ -69,7 +69,8 @@ class LoadData(speciesData.SpeciesData):
"""
"""
logging
.
debug
(
"
Getting
'
Homo sapiens
'
ID in chado database
"
)
logging
.
debug
(
"
Getting
'
Homo sapiens
'
ID in chado database
"
)
get_sapiens_id_job_output_dataset_id
=
utilities
.
run_tool_and_get_single_output_dataset_id
(
self
.
instance
,
get_sapiens_id_job_output_dataset_id
=
utilities
.
run_tool_and_get_single_output_dataset_id
(
self
.
instance
,
tool_id
=
constants
.
GET_ORGANISMS_TOOL
,
# If this version if not found, Galaxy will use the one that is found
tool_id
=
constants
.
GET_ORGANISMS_TOOL
,
# If this version if not found, Galaxy will use the one that is found
history_id
=
self
.
history_id
,
history_id
=
self
.
history_id
,
tool_inputs
=
{
"
genus
"
:
"
Homo
"
,
"
species
"
:
"
sapiens
"
})
tool_inputs
=
{
"
genus
"
:
"
Homo
"
,
"
species
"
:
"
sapiens
"
})
...
@@ -80,6 +81,7 @@ class LoadData(speciesData.SpeciesData):
...
@@ -80,6 +81,7 @@ class LoadData(speciesData.SpeciesData):
get_sapiens_id_final_output
=
json
.
loads
(
get_sapiens_id_json_output
)[
0
]
get_sapiens_id_final_output
=
json
.
loads
(
get_sapiens_id_json_output
)[
0
]
sapiens_id
=
str
(
get_sapiens_id_final_output
[
"
organism_id
"
])
# needs to be str to be recognized by the chado tool
sapiens_id
=
str
(
get_sapiens_id_final_output
[
"
organism_id
"
])
# needs to be str to be recognized by the chado tool
utilities
.
run_tool
(
utilities
.
run_tool
(
self
.
instance
,
tool_id
=
constants
.
DELETE_ORGANISMS_TOOL
,
tool_id
=
constants
.
DELETE_ORGANISMS_TOOL
,
history_id
=
self
.
history_id
,
history_id
=
self
.
history_id
,
tool_inputs
=
{
"
organism
"
:
sapiens_id
})
tool_inputs
=
{
"
organism
"
:
sapiens_id
})
...
...
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