add gp-sans app (2e6e7265) · Commits · NDIP / Playground

trame/air-sans/air_sans/gpsans/init.py

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		from .main import main

		__all__ = [
		"main",
		]

trame/air-sans/air_sans/gpsans/core.py

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		import os
		import numpy
		import logging

		from trame.app import get_server
		from trame.decorators import TrameApp, change
		from trame.ui.vuetify import SinglePageWithDrawerLayout
		from trame.widgets import vuetify, plotly

		from .ui import (
		Directory,
		FileSelector,
		FigureControl,
		)

		from .visualization import Visualization
		from .utilities import galaxy


		logger = logging.getLogger(__name__)
		logger.setLevel(logging.INFO)

		# ---------------------------------------------------------
		# Engine class
		# ---------------------------------------------------------


		@TrameApp()
		class GpSans:
		def __init__(self, server=None, data=None):
		self.server = get_server(server, client_type="vue2")
		self._viz = Visualization(self.server)
		self._active_directory = None

		# CLI
		self.server.cli.add_argument(
		"--data",
		help="Path to browse",
		dest="data",
		default=".",
		)
		args, _ = self.server.cli.parse_known_args()
		if data is None:
		data = args.data

		self.state.user_file = None
		self.state.staff_file = None
		self.server.state.ipts = None
		self.state.data = None
		self.ui = self._build_ui()

		@property
		def state(self):
		return self.server.state

		@property
		def ctrl(self):
		return self.server.controller

		def run(self):
		user_file = self.server.state.user_file
		staff_file = self.server.state.staff_file
		ipts = self.server.state.ipts
		data = galaxy.run_gpsans(user_file,staff_file,ipts)
		self._viz.create_gpsans_fig(data)
		self.server.state.figure_ready = True

		def _build_ui(self):
		self.state.trame__title = "gp-sans"
		with SinglePageWithDrawerLayout(self.server) as layout:
		with layout.icon:
		vuetify.VIcon("mdi-bullseye")

		with layout.title as title:
		title.set_text("GP-SANS")
		title.classes = "font-weight-medium ml-0 pl-0"

		with layout.drawer as drawer:
		drawer.width = 350
		vuetify.VFileInput(
		label="User Input File",
		v_model=("user_file", None),
		)
		vuetify.VFileInput(
		label="Staff Input File",
		v_model=("staff_file", None),
		)
		vuetify.VTextField(
		label="IPTS Number",
		v_model=("ipts", None),
		)
		vuetify.VBtn("Run in Galaxy",icon=False, click=self.run)

		with layout.content:
		with vuetify.VContainer(
		fluid=True,
		classes="pa-0 fill-height",
		):
		self.ctrl.update_d11 = plotly.Figure(
		display_mode_bar=("false",),
		v_show=("figure_ready", False),
		).update

		return layout

trame/air-sans/air_sans/gpsans/main.py

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		from .core import GpSans


		def main(server=None, **kwargs):
		app = GpSans(server)
		app.server.start(**kwargs)


		if __name__ == "__main__":
		main()

trame/air-sans/air_sans/gpsans/ui.py

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		from trame.widgets import html, vuetify

		SUPPORTED_DEVICES = ["D11+","GP-SANS"]


		class AbstractCard(vuetify.VCard):
		def __init__(self, key, icon, title):
		super().__init__(
		# classes="mb-3",
		tile=True,
		)
		with self:
		with vuetify.VCardTitle(
		style="user-select: none;",
		hide_details=True,
		dense=True,
		dark=True,
		) as self._title:
		vuetify.VIcon(icon, classes="mr-1", color="grey darken-3")
		html.Div(title)
		vuetify.VDivider()
		self._content = vuetify.VCardText(classes="pa-1")
		class DirectoryDialog(vuetify.VDialog):
		def __init__(self, select_directory_fn):
		super().__init__(
		v_model=("directory_dialog", False),
		persistent=True,
		)
		with self:
		with vuetify.Template(
		v_slot_activator="{ on, attrs }",
		):
		with vuetify.VBtn(
		small=True,
		color="primary",
		dark=True,
		icon=True,
		v_bind="attrs",
		v_on="on",
		):
		vuetify.VIcon("mdi-folder")
		with vuetify.VCard(
		classes="ma-1 rounded elevation-8", style="min-width: 50vw;"
		):
		with vuetify.VCardTitle(
		classes="grey lighten-1 px-2 py-0 grey--text text--darken-3",
		style="user-select: none;",
		hide_details=True,
		dense=True,
		):
		html.Div("Select History")
		with vuetify.VCardText(
		classes="pa-1", style="height: 50vh; overflow: auto;"
		):
		vuetify.VTreeview(
		classes="mb-1",
		dense=True,
		hide_details=True,
		v_model=("dirtree", []),
		items=("dirs", []),
		item_text="name",
		activatable=True,
		item_key="id",
		open_on_click=True,
		return_object=True,
		update_active=(
		select_directory_fn,
		"[$event]",
		),
		)
		with vuetify.VCardActions(
		classes="py-1",
		hide_details=True,
		dense=True,
		):
		vuetify.VSpacer()
		with vuetify.VBtn(
		icon=True,
		dense=True,
		small=True,
		tile=True,
		color="error",
		click="directory_dialog = false",
		):
		vuetify.VIcon("mdi-cancel")
		with vuetify.VBtn(
		icon=True,
		dense=True,
		small=True,
		tile=True,
		color="success",
		click="directory_dialog = false",
		):
		vuetify.VIcon("mdi-check")


		class Directory(AbstractCard):
		def __init__(self, select_directory_fn):
		super().__init__("directory", "mdi-folder-eye-outline", "Galaxy History")
		with self._content:
		with vuetify.VRow(classes="px-0 py-1", align_self="center"):
		with vuetify.VCol(cols="1", align_self="center"):
		DirectoryDialog(select_directory_fn)
		with vuetify.VCol(cols="11"):
		vuetify.VTextField(
		classes="mb-1",
		dense=True,
		hide_details=True,
		readonly=True,
		outlined=True,
		disabled=True,
		type="string",
		v_model=("directory_label", None),
		)


		class FileSelector(AbstractCard):
		def __init__(self, file_selection):
		super().__init__("file", "mdi-application-outline", "Browse")
		with self._content as content:
		content.classes = "px-0 mx-0"
		content.style = "max-height: min(12rem, 40vh); overflow: auto;"
		with vuetify.VList(
		dense=True,
		hide_details=True,
		):
		with vuetify.VListItemGroup(
		v_model=("file_selected", None),
		color="primary",
		):
		with vuetify.VListItem(
		v_for="(item, index) in files",
		key="index",
		dense=True,
		hide_details=True,
		click=(file_selection, "[item]"),
		color="primary",
		style="min-height:10px",
		):
		with vuetify.VListItemIcon(classes="ma-0 mr-1"):
		vuetify.VIcon("mdi-file", x_small=True)
		with vuetify.VListItemContent(classes="pa-0"):
		vuetify.VListItemTitle("{{item['name']}}")


		class FigureControl(AbstractCard):
		def __init__(self):
		super().__init__("viz", "mdi-image-multiple-outline", "Image")
		with self._content:
		with vuetify.VRow(classes="pa-0 pt-1", dense=True, hide_details=True):
		with vuetify.VCol(cols="6"):
		vuetify.VSelect(
		v_model=("selectedRepresentation", "Heatmap"),
		items=("representations", ["Heatmap", "Contours", "Combined"]),
		label="Representation",
		dense=True,
		hide_details=True,
		outlined=True,
		)
		with vuetify.VCol(cols="6"):
		vuetify.VSelect(
		v_model=("selectedColor", "spectral"),
		items=(
		"colors",
		["spectral", "rdbu", "gray", "blackbody", "sunset"],
		),
		label="Colors",
		dense=True,
		hide_details=True,
		outlined=True,
		)
		with vuetify.VRow(classes="pa-0 pt-1", dense=True, hide_details=True):
		with vuetify.VCol(cols="6"):
		vuetify.VCheckbox(
		v_model=("contour_labels", True),
		label="Contour labels",
		dense=True,
		hide_details=True,
		)

trame/air-sans/air_sans/gpsans/utilities/init.py

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Empty file added.