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Adding new components and loginless mode #5

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167 changes: 160 additions & 7 deletions config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
version: '0.0.0'
SciViz:
auth:
mode: database
auth: False
component_interface:
static_variables:
s3_host: $CUSTOM_S3_HOST|s3.amazonaws.com
Expand All @@ -11,11 +10,86 @@ SciViz:
s3_bucket: $CUSTOM_S3_BUCKET|bucket_name
override: |
from pharus.component_interface import (type_map, PlotPlotlyStoredjsonComponent,
FileImageAttachComponent)
FileImageAttachComponent, NumpyEncoder)
import minio
import io
from flask import send_file

class DepthPeth(PlotPlotlyStoredjsonComponent):
def dj_query_route(self):
fetch_metadata = self.fetch_metadata
record = (fetch_metadata['query'] & self.restriction).fetch(limit=1,
*fetch_metadata['fetch_args'])
s3_client = minio.Minio(endpoint=self.static_variables['s3_host'],
region=self.static_variables['s3_region'],
access_key=self.static_variables['s3_access_key'],
secret_key=self.static_variables['s3_secret_key'],
secure=True)
peth_template = record[0][11]
color_scale = record[0][10]
z_range = record[0][9]
plot_xlim = record[0][8]
plot_ylim = record[0][7]
link = record[0][6]
compiled_link = s3_client.presigned_get_object(self.static_variables['s3_bucket'], link)
event = record[0][3]

peth_template['data'][0]['x'] = [plot_xlim[0]-0.2, plot_xlim[0]-0.1]
peth_template['data'][0]['y'] = [plot_ylim[0]-0.2]
peth_template['data'][0]['z'] = z_range
peth_template['data'][0]['colorscale'] = color_scale
peth_template['layout']['images'][0]['source'] = compiled_link
peth_template['layout']['images'][0]['sizex'] = plot_xlim[1] - plot_xlim[0]
peth_template['layout']['images'][0]['sizey'] = plot_ylim[1] - plot_ylim[0]
peth_template['layout']['images'][0]['x'] = plot_xlim[0]
peth_template['layout']['images'][0]['y'] = plot_ylim[1]
peth_template['layout']['xaxis']['range'] = plot_xlim
peth_template['layout']['yaxis']['range'] = plot_ylim
peth_template['layout']['title']['text'] = f"Depth PETH, aligned to {event} time"
return NumpyEncoder.dumps(peth_template)

class TrialDepthRaster(PlotPlotlyStoredjsonComponent):
def dj_query_route(self):
fetch_metadata = self.fetch_metadata
record = (fetch_metadata['query'] & self.restriction).fetch(limit=1,
*fetch_metadata['fetch_args'])
s3_client = minio.Minio(endpoint=self.static_variables['s3_host'],
region=self.static_variables['s3_region'],
access_key=self.static_variables['s3_access_key'],
secret_key=self.static_variables['s3_secret_key'],
secure=True)

tdr_template = record[0][15]
trial_contrast = record[0][13]
trial_feedback = record[0][12]
trial_movement = record[0][11]
trial_stim_off = record[0][10]
trial_stim_on = record[0][9]
plot_title = record[0][8]
plot_xlim = record[0][7]
plot_ylim = record[0][6]
link = record[0][5]
compiled_link = s3_client.presigned_get_object(self.static_variables['s3_bucket'], link)
tdr_template['data'][0]['x'] = plot_xlim
tdr_template['data'][0]['y'] = plot_ylim
tdr_template['data'][1]['x'] = [trial_stim_on, trial_stim_on]
tdr_template['data'][1]['y'] = plot_ylim
tdr_template['data'][2]['x'] = [trial_movement, trial_movement]
tdr_template['data'][2]['y'] = plot_ylim
tdr_template['data'][3]['x'] = [trial_feedback, trial_feedback]
tdr_template['data'][3]['y'] = plot_ylim
tdr_template['data'][4]['x'] = [trial_stim_off, trial_stim_off]
tdr_template['data'][4]['y'] = plot_ylim
tdr_template['layout']['xaxis']['range'] = plot_xlim
tdr_template['layout']['yaxis']['range'] = plot_ylim
tdr_template['layout']['title']['text'] = plot_title
tdr_template['layout']['images'][0]['source'] = compiled_link
tdr_template['layout']['images'][0]['sizex'] = plot_xlim[1] - plot_xlim[0]
tdr_template['layout']['images'][0]['sizey'] = plot_ylim[1] - plot_ylim[0]
tdr_template['layout']['images'][0]['x'] = plot_xlim[0]
tdr_template['layout']['images'][0]['y'] = plot_ylim[1]
return NumpyEncoder.dumps(tdr_template)

class PlotPlotlyRemoveFirst(PlotPlotlyStoredjsonComponent):
def dj_query_route(self):
fetch_metadata = self.fetch_metadata
Expand All @@ -40,7 +114,9 @@ SciViz:
return send_file(io.BytesIO(result.data), download_name=s3_relpath)

type_map = dict({'plot:plotly:remove_first': PlotPlotlyRemoveFirst,
'file:image:s3:global_pointer': FileImageS3GlobalPointerComponent},
'file:image:s3:global_pointer': FileImageS3GlobalPointerComponent,
'plot:DepthPeth': DepthPeth,
'plot:TrialDepthRaster': TrialDepthRaster},
**type_map)
pages:
Home:
Expand Down Expand Up @@ -297,7 +373,7 @@ SciViz:
route: /session_gif_query
x: 0
y: 8
height: 2
height: 5
width: 1
type: file:image:s3:global_pointer
restriction: >
Expand Down Expand Up @@ -351,6 +427,84 @@ SciViz:
type_map = dict({'file:image:s3:global_pointer': FileImageS3GlobalPointerComponent},
**type_map)
```
newgrid:
type: fixed
columns: 3
row_height: 80
components:
mybuttons:
x: 0
y: 0
height: 1
width: 1
type: radiobuttons
channel: mybuttons
content:
feedback: 'event=feedback'
movement: 'event=movement'
stim on: 'event=stim on'
depthPETH:
x: 0
y: 1
height: 6
width: 1
type: plot:DepthPeth
channels: [mybuttons]
route: /depthpeth
restriction: >
def restriction(**kwargs):
return dict(**kwargs)
dj_query: >
def dj_query(ibl_plotting_ephys):
q = ibl_plotting_ephys.DepthPeth * ibl_plotting_ephys.DepthPethTemplate
return dict(query=q, fetch_args=[])
TrialDepthRaster:
route: /TrialDepthRaster
x: 1
y: 1
height: 10
width: 2
type: plot:TrialDepthRaster
channels: [rasterslider, sliderbuttons]
restriction: >
def restriction(**kwargs):
return dict(**kwargs)
dj_query: >
def dj_query(ibl_plotting_ephys):
q = ibl_plotting_ephys.DepthRasterExampleTrial * ibl_plotting_ephys.DepthRasterTemplate
return dict(query=q, fetch_args=[])
rasterslider:
x: 1
y: 0
height: 1
width: 1
route: /rasterslider
type: slider
channels: [sliderbuttons]
channel: rasterslider
restriction: >
def restriction(**kwargs):
return dict(**kwargs)
dj_query: >
def dj_query(ibl_plotting_ephys):
q = ibl_plotting_ephys.DepthRasterExampleTrial
return dict(query=q, fetch_args=['subject_uuid', 'session_start_time', 'probe_idx', 'trial_id', 'trial_contrast'])
sliderbuttons:
x: 2
y: 0
height: 1
width: 1
type: dropdown-static
channel: sliderbuttons
content:
'-1': 'trial_contrast=-1'
'-0.25': 'trial_contrast=-0.25'
'-0.125': 'trial_contrast=-0.125'
'-0.0625': 'trial_contrast=-0.0625'
'0.0625': 'trial_contrast=0.0625'
'0.125': 'trial_contrast=0.125'
'0.25': 'trial_contrast=0.25'
'1': 'trial_contrast=1'
Psychometric Curves:
route: /psychometric_curves
grids:
Expand Down Expand Up @@ -407,5 +561,4 @@ SciViz:
return dict(**kwargs)
dj_query: >
def dj_query(ibl_plotting_behavior):
return dict(query=ibl_plotting_behavior.SessionPsychCurve(), fetch_args=['plotting_data'])

return dict(query=ibl_plotting_behavior.SessionPsychCurve(), fetch_args=['plotting_data'])
6 changes: 4 additions & 2 deletions docker-compose.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,15 +11,17 @@ services:
environment:
PHARUS_SPEC_PATH: /main/specs/config.yaml # for dynamic api spec
PHARUS_MODE: ${MODE} # DEV | PROD
PHARUS_USER:
PHARUS_HOST:
PHARUS_PASSWORD:
env_file: .env
volumes:
- ./config.yaml:/main/specs/config.yaml:ro #copy the spec over to /main/specs/YOUR_SPEC_NAME
command:
- sh
- -c
- |
export PHARUS_PRIVATE_KEY=$$(echo $$PHARUS_PRIVATE_KEY | sed 's|\\n|\n|g')
otumat watch -f $${PHARUS_SPEC_PATH} -s /tmp/reload.sh -i 5
gunicorn --bind 0.0.0.0:$${PHARUS_PORT} pharus.server:app
# ports:
# - "5000:5000"
networks:
Expand Down