Add pyzebra handler

* allow user to specify anatric path

pyzebra/anatric.py

@@ -2,7 +2,6 @@ import subprocess
 import xml.etree.ElementTree as ET
 
 
-ANATRIC_PATH = "/afs/psi.ch/project/sinq/rhel7/bin/anatric"
 DATA_FACTORY_IMPLEMENTATION = [
     "trics",
     "morph",
@@ -24,8 +23,8 @@ REFLECTION_PRINTER_FORMATS = [
 ALGORITHMS = ["adaptivemaxcog", "adaptivedynamic"]
 
 
-def anatric(config_file):
-    subprocess.run([ANATRIC_PATH, config_file], check=True)
+def anatric(config_file, anatric_path="/afs/psi.ch/project/sinq/rhel7/bin/anatric"):
+    subprocess.run([anatric_path, config_file], check=True)
 
 
 class AnatricConfig:

pyzebra/app/app.py

-import argparse
 import logging
 import sys
 from io import StringIO
@@ -11,14 +10,8 @@ import panel_ccl_integrate
 import panel_hdf_anatric
 import panel_hdf_viewer
 
-parser = argparse.ArgumentParser(
-    prog="pyzebra", formatter_class=argparse.ArgumentDefaultsHelpFormatter
-)
-
-args = parser.parse_args()
 
 doc = curdoc()
-doc.title = "pyzebra"
 
 sys.stdout = StringIO()
 stdout_textareainput = TextAreaInput(title="print output:", height=150)
@@ -26,7 +19,7 @@ stdout_textareainput = TextAreaInput(title="print output:", height=150)
 bokeh_stream = StringIO()
 bokeh_handler = logging.StreamHandler(bokeh_stream)
 bokeh_handler.setFormatter(logging.Formatter(logging.BASIC_FORMAT))
-bokeh_logger = logging.getLogger('bokeh')
+bokeh_logger = logging.getLogger("bokeh")
 bokeh_logger.addHandler(bokeh_handler)
 bokeh_log_textareainput = TextAreaInput(title="server output:", height=150)
 

pyzebra/app/handler.py

+from bokeh.application.handlers import Handler
+
+
+class PyzebraHandler(Handler):
+    """Provides a mechanism for generic bokeh applications to build up new streamvis documents.
+    """
+
+    def __init__(self, anatric_path):
+        """Initialize a pyzebra handler for bokeh applications.
+
+        Args:
+            args (Namespace): Command line parsed arguments.
+        """
+        super().__init__()  # no-op
+
+        self.anatric_path = anatric_path
+
+    def modify_document(self, doc):
+        """Modify an application document with pyzebra specific features.
+
+        Args:
+            doc (Document) : A bokeh Document to update in-place
+
+        Returns:
+            Document
+        """
+        doc.title = "pyzebra"
+        doc.anatric_path = self.anatric_path
+
+        return doc

pyzebra/app/panel_hdf_anatric.py

@@ -21,6 +21,7 @@ from pyzebra.anatric import DATA_FACTORY_IMPLEMENTATION, REFLECTION_PRINTER_FORM
 
 
 def create():
+    doc = curdoc()
     config = pyzebra.AnatricConfig()
 
     def _load_config_file(file):
@@ -345,7 +346,7 @@ def create():
         with tempfile.TemporaryDirectory() as temp_dir:
             temp_file = temp_dir + "/temp.xml"
             config.save_as(temp_file)
-            pyzebra.anatric(temp_file)
+            pyzebra.anatric(temp_file, anatric_path=doc.anatric_path)
 
             with open(config.logfile) as f_log:
                 output_log.value = f_log.read()
@@ -404,6 +405,6 @@ def create():
         with open("debug.xml") as f_config:
             output_config.value = f_config.read()
 
-    curdoc().add_periodic_callback(update_config, 1000)
+    doc.add_periodic_callback(update_config, 1000)
 
     return Panel(child=tab_layout, title="hdf anatric")

pyzebra/cli.py

@@ -6,6 +6,8 @@ from bokeh.application.application import Application
 from bokeh.application.handlers import ScriptHandler
 from bokeh.server.server import Server
 
+from pyzebra.app.handler import PyzebraHandler
+
 logging.basicConfig(format="%(asctime)s %(message)s", level=logging.INFO)
 logger = logging.getLogger(__name__)
 
@@ -35,6 +37,13 @@ def main():
         help="hostname that can connect to the server websocket",
     )
 
+    parser.add_argument(
+        "--anatric-path",
+        type=str,
+        default="/afs/psi.ch/project/sinq/rhel7/bin/anatric",
+        help="path to anatric executable",
+    )
+
     parser.add_argument(
         "--args",
         nargs=argparse.REMAINDER,
@@ -46,9 +55,10 @@ def main():
 
     logger.info(app_path)
 
+    pyzebra_handler = PyzebraHandler(args.anatric_path)
     handler = ScriptHandler(filename=app_path, argv=args.args)
     server = Server(
-        {"/": Application(handler)},
+        {"/": Application(pyzebra_handler, handler)},
         port=args.port,
         allow_websocket_origin=args.allow_websocket_origin,
     )