Switch to bokeh wrapper for app serving
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17
pyzebra/app/app_hooks.py
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17
pyzebra/app/app_hooks.py
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@ -0,0 +1,17 @@
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import logging
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import sys
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from io import StringIO
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def on_server_loaded(_server_context):
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formatter = logging.Formatter(
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fmt="%(asctime)s %(levelname)s: %(message)s", datefmt="%Y-%m-%d %H:%M:%S"
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)
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sys.stdout = StringIO()
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bokeh_handler = logging.StreamHandler(StringIO())
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bokeh_handler.setFormatter(formatter)
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bokeh_logger = logging.getLogger("bokeh")
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bokeh_logger.setLevel(logging.WARNING)
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bokeh_logger.addHandler(bokeh_handler)
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@ -1,77 +1,11 @@
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import argparse
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import logging
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import os
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from bokeh.application.application import Application
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from bokeh.application.handlers import ScriptHandler
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from bokeh.server.server import Server
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from pyzebra import ANATRIC_PATH, SXTAL_REFGEN_PATH
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from pyzebra.app.handler import PyzebraHandler
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logging.basicConfig(format="%(asctime)s %(message)s", level=logging.INFO)
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logger = logging.getLogger(__name__)
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import subprocess
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import sys
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def main():
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"""The pyzebra command line interface.
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This is a wrapper around a bokeh server that provides an interface to launch the application,
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bundled with the pyzebra package.
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"""
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app_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "app.py")
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parser = argparse.ArgumentParser(
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prog="pyzebra", formatter_class=argparse.ArgumentDefaultsHelpFormatter
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)
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parser.add_argument(
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"--port", type=int, default=5006, help="port to listen on for HTTP requests"
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)
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parser.add_argument(
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"--allow-websocket-origin",
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metavar="HOST[:PORT]",
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type=str,
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action="append",
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default=None,
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help="hostname that can connect to the server websocket",
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)
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parser.add_argument(
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"--anatric-path", type=str, default=ANATRIC_PATH, help="path to anatric executable"
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)
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parser.add_argument(
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"--sxtal-refgen-path",
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type=str,
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default=SXTAL_REFGEN_PATH,
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help="path to Sxtal_Refgen executable",
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)
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parser.add_argument("--spind-path", type=str, default=None, help="path to spind scripts folder")
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parser.add_argument(
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"--args",
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nargs=argparse.REMAINDER,
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default=[],
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help="command line arguments for the pyzebra application",
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)
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args = parser.parse_args()
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logger.info(app_path)
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pyzebra_handler = PyzebraHandler(args.anatric_path, args.spind_path)
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handler = ScriptHandler(filename=app_path, argv=args.args)
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server = Server(
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{"/": Application(pyzebra_handler, handler)},
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port=args.port,
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allow_websocket_origin=args.allow_websocket_origin,
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)
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server.start()
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server.io_loop.start()
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app_path = os.path.join(os.path.dirname(os.path.abspath(__file__)))
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subprocess.run(["bokeh", "serve", app_path, *sys.argv[1:]], check=True)
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if __name__ == "__main__":
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@ -1,31 +0,0 @@
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from bokeh.application.handlers import Handler
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class PyzebraHandler(Handler):
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"""Provides a mechanism for generic bokeh applications to build up new streamvis documents."""
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def __init__(self, anatric_path, spind_path):
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"""Initialize a pyzebra handler for bokeh applications.
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Args:
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args (Namespace): Command line parsed arguments.
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"""
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super().__init__() # no-op
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self.anatric_path = anatric_path
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self.spind_path = spind_path
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def modify_document(self, doc):
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"""Modify an application document with pyzebra specific features.
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Args:
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doc (Document) : A bokeh Document to update in-place
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Returns:
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Document
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"""
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doc.title = "pyzebra"
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doc.anatric_path = self.anatric_path
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doc.spind_path = self.spind_path
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return doc
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@ -1,6 +1,6 @@
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import argparse
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import logging
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import sys
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from io import StringIO
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from bokeh.io import curdoc
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from bokeh.layouts import column, row
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@ -20,16 +20,33 @@ from pyzebra.app import (
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)
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doc = curdoc()
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doc.title = "pyzebra"
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sys.stdout = StringIO()
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stdout_textareainput = TextAreaInput(title="print output:")
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parser = argparse.ArgumentParser()
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bokeh_stream = StringIO()
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bokeh_handler = logging.StreamHandler(bokeh_stream)
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bokeh_handler.setFormatter(logging.Formatter(logging.BASIC_FORMAT))
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bokeh_logger = logging.getLogger("bokeh")
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bokeh_logger.setLevel(logging.WARNING)
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bokeh_logger.addHandler(bokeh_handler)
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parser.add_argument(
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"--anatric-path", type=str, default=pyzebra.ANATRIC_PATH, help="path to anatric executable"
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)
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parser.add_argument(
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"--sxtal-refgen-path",
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type=str,
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default=pyzebra.SXTAL_REFGEN_PATH,
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help="path to Sxtal_Refgen executable",
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)
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parser.add_argument("--spind-path", type=str, default=None, help="path to spind scripts folder")
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args = parser.parse_args()
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doc.anatric_path = args.anatric_path
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doc.spind_path = args.spind_path
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doc.sxtal_refgen_path = args.sxtal_refgen_path
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# In app_hooks.py a StreamHandler was added to "bokeh" logger
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bokeh_stream = logging.getLogger("bokeh").handlers[0].stream
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log_textareainput = TextAreaInput(title="logging output:")
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bokeh_log_textareainput = TextAreaInput(title="server output:")
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@ -77,13 +94,13 @@ doc.add_root(
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panel_spind.create(),
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]
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),
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row(stdout_textareainput, bokeh_log_textareainput, sizing_mode="scale_both"),
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row(log_textareainput, bokeh_log_textareainput, sizing_mode="scale_both"),
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)
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)
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def update_stdout():
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stdout_textareainput.value = sys.stdout.getvalue()
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log_textareainput.value = sys.stdout.getvalue()
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bokeh_log_textareainput.value = bokeh_stream.getvalue()
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@ -1,4 +1,4 @@
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source /opt/miniconda3/etc/profile.d/conda.sh
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conda activate test
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python /opt/pyzebra/pyzebra/app/cli.py --port=5010 --allow-websocket-origin=pyzebra.psi.ch:5010 --spind-path=/opt/spind
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python /opt/pyzebra/pyzebra/app/cli.py --port=5010 --allow-websocket-origin=pyzebra.psi.ch:5010 --args --spind-path=/opt/spind
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@ -1,4 +1,4 @@
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source /opt/miniconda3/etc/profile.d/conda.sh
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conda activate prod
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pyzebra --port=80 --allow-websocket-origin=pyzebra.psi.ch:80 --spind-path=/opt/spind
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pyzebra --port=80 --allow-websocket-origin=pyzebra.psi.ch:80 --args --spind-path=/opt/spind
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