Replaced most other instances of URL requests to the instrument or backend servers to 'url_path_for'

Author: tieneupin

src/murfey/bootstrap/__main__.py

@@ -7,9 +7,11 @@
 import pathlib
 import subprocess
 import sys
-from urllib.parse import urlparse
+from urllib.parse import ParseResult, urlparse
 from urllib.request import urlopen
 
+from murfey.util.api import url_path_for
+
 """
 A script to simplify installing Murfey on a network-isolated machine.
 This could in theory be invoked by
@@ -64,10 +66,13 @@ def _download_to_file(url: str, outfile: str):
     # Construct a minimal base path string
     # Extract the host name for pip installation purposes
     try:
-        murfey_url = urlparse(args.server)
+        murfey_url: ParseResult = urlparse(args.server)
     except Exception:
         exit(f"{args.server} is not a valid URL")
+    murfey_proxy_path = murfey_url.path.rstrip("/")
     murfey_base = f"{murfey_url.scheme}://{murfey_url.netloc}"
+    if murfey_proxy_path:
+        murfey_base = f"{murfey_base}{murfey_proxy_path}"
     murfey_hostname = murfey_url.netloc.split(":")[0]
 
     # Check that Python version is supported
@@ -82,7 +87,10 @@ def _download_to_file(url: str, outfile: str):
     # Step 1: Download pip wheel
     print()
     print(f"1/4 -- Connecting to murfey server on {murfey_base}...")
-    _download_to_file(f"{murfey_base}/bootstrap/pip.whl", "pip.whl")
+    _download_to_file(
+        f"{murfey_base}{url_path_for('bootstrap.bootstrap', 'get_pip_wheel')}",
+        "pip.whl",
+    )
 
     # Step 2: Get pip to install itself
     print()
@@ -96,7 +104,7 @@ def _download_to_file(url: str, outfile: str):
             "--trusted-host",
             murfey_hostname,
             "-i",
-            f"{murfey_base}/pypi",
+            f"{murfey_base}{url_path_for('bootstrap.pypi', 'get_pypi_index')}",
             "pip",
         ]
     )
@@ -116,7 +124,7 @@ def _download_to_file(url: str, outfile: str):
             "--trusted-host",
             murfey_hostname,
             "-i",
-            f"{murfey_base}/pypi",
+            f"{murfey_base}{url_path_for('bootstrap.pypi', 'get_pypi_index')}",
             "--upgrade",
             "pip",
         ]
@@ -135,7 +143,7 @@ def _download_to_file(url: str, outfile: str):
             "--trusted-host",
             murfey_hostname,
             "-i",
-            f"{murfey_base}/pypi",
+            f"{murfey_base}{url_path_for('bootstrap.pypi', 'get_pypi_index')}",
             "murfey[client]",
         ]
     )

src/murfey/cli/spa_ispyb_messages.py

@@ -22,6 +22,7 @@
 from murfey.server.ispyb import ISPyBSession, TransportManager, get_session_id
 from murfey.server.murfey_db import url
 from murfey.util import db
+from murfey.util.api import url_path_for
 from murfey.util.config import get_machine_config, get_microscope, get_security_config
 
 
@@ -69,7 +70,7 @@ def run():
         help="Path to directory containing image files",
     )
     parser.add_argument(
-        "--suffic",
+        "--suffix",
         dest="suffix",
         required=True,
         type=str,
@@ -203,7 +204,9 @@ def run():
         ]
     )
     binning_factor = 1
-    server_config = requests.get(f"{args.url}/machine").json()
+    server_config = requests.get(
+        f"{args.url}{url_path_for('session_control.router', 'machine_info_by_instrument', instrument_name=args.microscope)}"
+    ).json()
     if server_config.get("superres"):
         # If camera is capable of superres and collection is in superres
         binning_factor = 2

src/murfey/cli/transfer.py

@@ -3,13 +3,14 @@
 import argparse
 import subprocess
 from pathlib import Path
-from urllib.parse import urlparse
+from urllib.parse import ParseResult, urlparse
 
 import requests
 from rich.console import Console
 from rich.prompt import Confirm
 
 from murfey.client import read_config
+from murfey.util.api import url_path_for
 from murfey.util.config import MachineConfig
 
 
@@ -35,11 +36,11 @@ def run():
     args = parser.parse_args()
 
     console = Console()
-    murfey_url = urlparse(args.server, allow_fragments=False)
+    murfey_url: ParseResult = urlparse(args.server, allow_fragments=False)
 
     machine_data = MachineConfig(
         requests.get(
-            f"{murfey_url.geturl()}/instruments/{instrument_name}/machine"
+            f"{murfey_url.geturl()}{url_path_for('session_control.router', 'machine_info_by_instrument', instrument_name=instrument_name)}"
         ).json()
     )
     if Path(args.source or ".").resolve() in machine_data.data_directories:

src/murfey/client/__init__.py

@@ -275,7 +275,9 @@ def run():
     rich_handler.setLevel(logging.DEBUG if args.debug else logging.INFO)
 
     # Set up websocket app and handler
-    client_id = requests.get(f"{murfey_url.geturl()}/new_client_id/").json()
+    client_id = requests.get(
+        f"{murfey_url.geturl()}{url_path_for('session_control.router', 'new_client_id')}"
+    ).json()
     ws = murfey.client.websocket.WSApp(
         server=args.server,
         id=client_id["new_id"],
@@ -292,7 +294,7 @@ def run():
 
     # Load machine data for subsequent sections
     machine_data = requests.get(
-        f"{murfey_url.geturl()}/instruments/{instrument_name}/machine"
+        f"{murfey_url.geturl()}{url_path_for('session_control.router', 'machine_info_by_instrument', instrument_name=instrument_name)}"
     ).json()
     gain_ref: Path | None = None
 

src/murfey/client/contexts/clem.py

@@ -14,6 +14,7 @@
 
 from murfey.client.context import Context
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
+from murfey.util.api import url_path_for
 from murfey.util.client import capture_post, get_machine_config_client
 
 # Create logger object
@@ -351,7 +352,7 @@ def register_lif_file(
         """
         try:
             # Construct URL to post to post the request to
-            url = f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/clem/lif_files?lif_file={quote(str(lif_file), safe='')}"
+            url = f"{environment.url.geturl()}{url_path_for('clem.router', 'register_lif_file', session_id=environment.murfey_session)}?lif_file={quote(str(lif_file), safe='')}"
             # Validate
             if not url:
                 logger.error(
@@ -381,7 +382,7 @@ def process_lif_file(
 
         try:
             # Construct the URL to post the request to
-            url = f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/clem/preprocessing/process_raw_lifs?lif_file={quote(str(lif_file), safe='')}"
+            url = f"{environment.url.geturl()}{url_path_for('clem.router', 'process_raw_lifs', session_id=environment.murfey_session)}?lif_file={quote(str(lif_file), safe='')}"
             # Validate
             if not url:
                 logger.error(
@@ -408,7 +409,7 @@ def register_tiff_file(
         """
 
         try:
-            url = f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/clem/tiff_files?tiff_file={quote(str(tiff_file), safe='')}"
+            url = f"{environment.url.geturl()}{url_path_for('clem.router', 'register_tiff_file', session_id=environment.murfey_session)}?tiff_file={quote(str(tiff_file), safe='')}"
             if not url:
                 logger.error(
                     "URL could not be constructed from the environment and file path"
@@ -437,7 +438,7 @@ def process_tiff_series(
 
         try:
             # Construct URL for Murfey server to communicate with
-            url = f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/clem/preprocessing/process_raw_tiffs"
+            url = f"{environment.url.geturl()}{url_path_for('clem.router', 'process_raw_tiffs', session_id=environment.murfey_session)}"
             if not url:
                 logger.error(
                     "URL could not be constructed from the environment and file path"

src/murfey/client/contexts/fib.py

@@ -10,6 +10,7 @@
 
 from murfey.client.context import Context
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
+from murfey.util.api import url_path_for
 from murfey.util.client import authorised_requests
 
 logger = logging.getLogger("murfey.client.contexts.fib")
@@ -95,7 +96,7 @@ def post_transfer(
                     ).name
                     # post gif list to gif making API call
                     requests.post(
-                        f"{str(environment.url.geturl())}/visits/{datetime.now().year}/{environment.visit}/{environment.murfey_session}/make_milling_gif",
+                        f"{environment.url.geturl()}{url_path_for('workflow.correlative_router', 'make_gif', year=datetime.now().year, visit_name=environment.visit, session_id=environment.murfey_session)}",
                         json={
                             "lamella_number": lamella_number,
                             "images": gif_list,

src/murfey/client/contexts/spa.py

@@ -405,7 +405,7 @@ def _position_analysis(
             ] = (None, None, None, None, None, None, None)
             data_collection_group = (
                 requests.get(
-                    f"{str(environment.url.geturl())}/sessions/{environment.murfey_session}/data_collection_groups"
+                    f"{environment.url.geturl()}{url_path_for('session_info.router', 'get_dc_groups', session_id=environment.murfey_session)}"
                 )
                 .json()
                 .get(str(source), {})
@@ -567,7 +567,7 @@ def post_transfer(
                         )
                         if not environment.movie_counters.get(str(source)):
                             movie_counts_get = capture_get(
-                                f"{str(environment.url.geturl())}/num_movies",
+                                f"{environment.url.geturl()}{url_path_for('session_info.router', 'count_number_of_movies')}",
                             )
                             if movie_counts_get is not None:
                                 environment.movie_counters[str(source)] = count(

src/murfey/client/multigrid_control.py

@@ -63,7 +63,7 @@ def __post_init__(self):
                 requests.delete, headers={"Authorization": f"Bearer {self.token}"}
             )
         machine_data = requests.get(
-            f"{self.murfey_url}/instruments/{self.instrument_name}/machine"
+            f"{self.murfey_url}{url_path_for('session_control.router', 'machine_info_by_instrument', instrument_name=self.instrument_name)}"
         ).json()
         self.rsync_url = machine_data.get("rsync_url", "")
         self.rsync_module = machine_data.get("rsync_module", "data")
@@ -209,10 +209,10 @@ def _start_rsyncer_multigrid(
 
     def _rsyncer_stopped(self, source: Path, explicit_stop: bool = False):
         if explicit_stop:
-            remove_url = f"{self.murfey_url}/sessions/{self.session_id}/rsyncer?source={quote(str(source), safe='')}"
+            remove_url = f"{self.murfey_url}{url_path_for('session_control.router', 'delete_rsyncer', session_id=self.session_id)}?source={quote(str(source), safe='')}"
             requests.delete(remove_url)
         else:
-            stop_url = f"{self.murfey_url}/sessions/{self.session_id}/rsyncer_stopped"
+            stop_url = f"{self.murfey_url}{url_path_for('session_control.router', 'register_stopped_rsyncer', session_id=self.session_id)}"
             capture_post(stop_url, json={"source": str(source)})
 
     def _finalise_rsyncer(self, source: Path):
@@ -228,7 +228,7 @@ def _finalise_rsyncer(self, source: Path):
 
     def _restart_rsyncer(self, source: Path):
         self.rsync_processes[source].restart()
-        restarted_url = f"{self.murfey_url}/sessions/{self.session_id}/rsyncer_started"
+        restarted_url = f"{self.murfey_url}{url_path_for('session_control.router', 'register_restarted_rsyncer', session_id=self.session_id)}"
         capture_post(restarted_url, json={"source": str(source)})
 
     def _request_watcher_stop(self, source: Path):
@@ -251,9 +251,7 @@ def _start_rsyncer(
         log.info(f"starting rsyncer: {source}")
         if transfer:
             # Always make sure the destination directory exists
-            make_directory_url = (
-                f"{self.murfey_url}/sessions/{self.session_id}/make_rsyncer_destination"
-            )
+            make_directory_url = f"{self.murfey_url}{url_path_for('file_manip.router', 'make_rsyncer_destination', session_id=self.session_id)}"
             capture_post(make_directory_url, json={"destination": destination})
         if self._environment:
             self._environment.default_destinations[source] = destination
@@ -323,12 +321,10 @@ def rsync_result(update: RSyncerUpdate):
                 secondary=True,
             )
             if restarted:
-                restarted_url = (
-                    f"{self.murfey_url}/sessions/{self.session_id}/rsyncer_started"
-                )
+                restarted_url = f"{self.murfey_url}{url_path_for('session_control.router', 'register_restarted_rsyncer', session_id=self.session_id)}"
                 capture_post(restarted_url, json={"source": str(source)})
             else:
-                url = f"{str(self._environment.url.geturl())}/sessions/{str(self._environment.murfey_session)}/rsyncer"
+                url = f"{str(self._environment.url.geturl())}{url_path_for('session_control.router', 'register_rsyncer', session_id=self._environment.murfey_session)}"
                 rsyncer_data = {
                     "source": str(source),
                     "destination": destination,

src/murfey/client/tui/app.py

@@ -621,7 +621,7 @@ async def on_button_pressed(self, event: Button.Pressed):
 
     async def on_mount(self) -> None:
         exisiting_sessions = requests.get(
-            f"{self._environment.url.geturl()}/sessions"
+            f"{self._environment.url.geturl()}{url_path_for('session_control.router', 'get_sessions')}"
         ).json()
         if self.visits:
             self.install_screen(VisitSelection(self.visits), "visit-select-screen")

src/murfey/client/tui/screens.py

@@ -699,12 +699,12 @@ def on_button_pressed(self, event: Button.Pressed):
         self.app._visit = text
         self.app._environment.visit = text
         response = requests.post(
-            f"{self.app._environment.url.geturl()}/visits/{text}",
+            f"{self.app._environment.url.geturl()}{url_path_for('session_control.router', 'register_client_to_visit', visit_name=text)}",
             json={"id": self.app._environment.client_id},
         )
         log.info(f"Posted visit registration: {response.status_code}")
         machine_data = requests.get(
-            f"{self.app._environment.url.geturl()}/instruments/{instrument_name}/machine"
+            f"{self.app._environment.url.geturl()}{url_path_for('session_control.router', 'machine_info_by_instrument', instrument_name=instrument_name)}"
         ).json()
 
         if self._switch_status:
@@ -766,7 +766,7 @@ def on_button_pressed(self, event: Button.Pressed):
         self.app._visit = text
         self.app._environment.visit = text
         response = requests.post(
-            f"{self.app._environment.url.geturl()}/visits/{text}",
+            f"{self.app._environment.url.geturl()}{url_path_for('session_control.router', 'register_client_to_visit', visit_name=text)}",
             json={"id": self.app._environment.client_id},
         )
         log.info(f"Posted visit registration: {response.status_code}")