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Cosy-Bio
Drugst.One
backend
Commits
ac2bd8b1
Commit
ac2bd8b1
authored
2 years ago
by
AndiMajore
Browse files
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Patches
Plain Diff
fixed network export
parent
009a4fc7
No related branches found
No related tags found
No related merge requests found
Pipeline
#12039
failed
2 years ago
Stage: check
Changes
2
Pipelines
1
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2 changed files
drugstone/views.py
+20
-10
20 additions, 10 deletions
drugstone/views.py
scripts/docker-entrypoint.sh
+1
-1
1 addition, 1 deletion
scripts/docker-entrypoint.sh
with
21 additions
and
11 deletions
drugstone/views.py
+
20
−
10
View file @
ac2bd8b1
...
@@ -20,7 +20,8 @@ from drugstone import models
...
@@ -20,7 +20,8 @@ from drugstone import models
from
drugstone
import
serializers
from
drugstone
import
serializers
from
drugstone.models
import
Protein
,
Task
,
ProteinDrugInteraction
,
\
from
drugstone.models
import
Protein
,
Task
,
ProteinDrugInteraction
,
\
Drug
,
Tissue
,
ExpressionLevel
,
Network
,
ProteinDisorderAssociation
,
DrugDisorderIndication
,
Disorder
,
DrDiDataset
,
PDIDataset
,
PDisDataset
,
PPIDataset
Drug
,
Tissue
,
ExpressionLevel
,
Network
,
ProteinDisorderAssociation
,
DrugDisorderIndication
,
Disorder
,
DrDiDataset
,
\
PDIDataset
,
PDisDataset
,
PPIDataset
from
drugstone.serializers
import
ProteinSerializer
,
TaskSerializer
,
\
from
drugstone.serializers
import
ProteinSerializer
,
TaskSerializer
,
\
ProteinDrugInteractionSerializer
,
DrugSerializer
,
TaskStatusSerializer
,
TissueSerializer
,
NetworkSerializer
,
\
ProteinDrugInteractionSerializer
,
DrugSerializer
,
TaskStatusSerializer
,
TissueSerializer
,
NetworkSerializer
,
\
ProteinDisorderAssociationSerializer
,
DisorderSerializer
,
DrugDisorderIndicationSerializer
ProteinDisorderAssociationSerializer
,
DisorderSerializer
,
DrugDisorderIndicationSerializer
...
@@ -408,12 +409,15 @@ def result_view(request) -> Response:
...
@@ -408,12 +409,15 @@ def result_view(request) -> Response:
edge
[
'
to
'
]
=
nodes_mapped_dict
[
edge
[
'
to
'
]][
node_name_attribute
]
if
edge
[
'
to
'
]
in
nodes_mapped_dict
else
edge
[
edge
[
'
to
'
]
=
nodes_mapped_dict
[
edge
[
'
to
'
]][
node_name_attribute
]
if
edge
[
'
to
'
]
in
nodes_mapped_dict
else
edge
[
'
to
'
]
'
to
'
]
if
'
autofill_edges
'
in
parameters
[
'
config
'
]
and
parameters
[
'
config
'
][
'
autofill_edges
'
]:
if
'
autofill_edges
'
in
parameters
[
'
config
'
]
and
parameters
[
'
config
'
][
'
autofill_edges
'
]:
proteins
=
set
(
map
(
lambda
n
:
n
[
node_name_attribute
][
1
:],
filter
(
lambda
n
:
node_name_attribute
in
n
,
parameters
[
'
input_network
'
][
'
nodes
'
])))
proteins
=
set
(
map
(
lambda
n
:
n
[
node_name_attribute
][
1
:],
dataset
=
'
STRING
'
if
'
interaction_protein_protein
'
not
in
parameters
[
'
config
'
]
else
parameters
[
'
config
'
][
'
interaction_protein_protein
'
]
filter
(
lambda
n
:
node_name_attribute
in
n
,
parameters
[
'
input_network
'
][
'
nodes
'
])))
dataset
=
'
STRING
'
if
'
interaction_protein_protein
'
not
in
parameters
[
'
config
'
]
else
parameters
[
'
config
'
][
'
interaction_protein_protein
'
]
dataset_object
=
models
.
PPIDataset
.
objects
.
filter
(
name__iexact
=
dataset
).
last
()
dataset_object
=
models
.
PPIDataset
.
objects
.
filter
(
name__iexact
=
dataset
).
last
()
interaction_objects
=
models
.
ProteinProteinInteraction
.
objects
.
filter
(
interaction_objects
=
models
.
ProteinProteinInteraction
.
objects
.
filter
(
Q
(
ppi_dataset
=
dataset_object
)
&
Q
(
from_protein__in
=
proteins
)
&
Q
(
to_protein__in
=
proteins
))
Q
(
ppi_dataset
=
dataset_object
)
&
Q
(
from_protein__in
=
proteins
)
&
Q
(
to_protein__in
=
proteins
))
auto_edges
=
list
(
map
(
lambda
n
:
{
"
from
"
:
f
'
p
{
n
.
from_protein_id
}
'
,
"
to
"
:
f
'
p
{
n
.
to_protein_id
}
'
}
,
interaction_objects
))
auto_edges
=
list
(
map
(
lambda
n
:
{
"
from
"
:
f
'
p
{
n
.
from_protein_id
}
'
,
"
to
"
:
f
'
p
{
n
.
to_protein_id
}
'
},
interaction_objects
))
edges
.
extend
(
auto_edges
)
edges
.
extend
(
auto_edges
)
result
[
'
network
'
][
'
edges
'
].
extend
(
edges
)
result
[
'
network
'
][
'
edges
'
].
extend
(
edges
)
...
@@ -471,7 +475,7 @@ def graph_export(request) -> Response:
...
@@ -471,7 +475,7 @@ def graph_export(request) -> Response:
edges
=
request
.
data
.
get
(
'
edges
'
,
[])
edges
=
request
.
data
.
get
(
'
edges
'
,
[])
fmt
=
request
.
data
.
get
(
'
fmt
'
,
'
graphml
'
)
fmt
=
request
.
data
.
get
(
'
fmt
'
,
'
graphml
'
)
G
=
nx
.
Graph
()
G
=
nx
.
Graph
()
node_map
=
dict
()
for
node
in
nodes
:
for
node
in
nodes
:
# drugstone_id is not interesting outside of drugstone
# drugstone_id is not interesting outside of drugstone
# try:
# try:
...
@@ -487,6 +491,10 @@ def graph_export(request) -> Response:
...
@@ -487,6 +491,10 @@ def graph_export(request) -> Response:
node
[
key
]
=
''
node
[
key
]
=
''
try
:
try
:
node_name
=
node
[
'
label
'
]
node_name
=
node
[
'
label
'
]
if
'
drugstone_id
'
in
node
:
node_map
[
node
[
'
drugstone_id
'
]]
=
node
[
'
label
'
]
elif
'
id
'
in
node
:
node_map
[
node
[
'
id
'
]]
=
node
[
'
label
'
]
except
KeyError
:
except
KeyError
:
node_name
=
node
[
'
drugstone_id
'
]
node_name
=
node
[
'
drugstone_id
'
]
G
.
add_node
(
node_name
,
**
node
)
G
.
add_node
(
node_name
,
**
node
)
...
@@ -498,9 +506,11 @@ def graph_export(request) -> Response:
...
@@ -498,9 +506,11 @@ def graph_export(request) -> Response:
e
[
key
]
=
json
.
dumps
(
e
[
key
])
e
[
key
]
=
json
.
dumps
(
e
[
key
])
elif
e
[
key
]
is
None
:
elif
e
[
key
]
is
None
:
e
[
key
]
=
''
e
[
key
]
=
''
u_of_edgece
=
e
.
pop
(
'
from
'
)
u_of_edge
=
e
.
pop
(
'
from
'
)
u_of_edge
=
u_of_edge
if
u_of_edge
not
in
node_map
else
node_map
[
u_of_edge
]
v_of_edge
=
e
.
pop
(
'
to
'
)
v_of_edge
=
e
.
pop
(
'
to
'
)
G
.
add_edge
(
u_of_edgece
,
v_of_edge
,
**
e
)
v_of_edge
=
node_map
[
v_of_edge
]
if
v_of_edge
in
node_map
else
v_of_edge
G
.
add_edge
(
u_of_edge
,
v_of_edge
,
**
e
)
if
fmt
==
'
graphml
'
:
if
fmt
==
'
graphml
'
:
data
=
nx
.
generate_graphml
(
G
)
data
=
nx
.
generate_graphml
(
G
)
...
...
This diff is collapsed.
Click to expand it.
scripts/docker-entrypoint.sh
+
1
−
1
View file @
ac2bd8b1
...
@@ -4,7 +4,7 @@ python3 manage.py makemigrations drugstone
...
@@ -4,7 +4,7 @@ python3 manage.py makemigrations drugstone
python3 manage.py migrate
python3 manage.py migrate
python3 manage.py createfixtures
python3 manage.py createfixtures
python3 manage.py cleanuptasks
python3 manage.py cleanuptasks
python3 manage.py populate_db
--update
-a
#
python3 manage.py populate_db --update -a
#python3 manage.py make_graphs
#python3 manage.py make_graphs
/usr/bin/supervisord
-c
"/etc/supervisor/conf.d/supervisord.conf"
/usr/bin/supervisord
-c
"/etc/supervisor/conf.d/supervisord.conf"
This diff is collapsed.
Click to expand it.
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