bec-server 2.4.2__tar.gz → 2.6.0__tar.gz

bec_server-2.6.0/.gitignore

@@ -0,0 +1,180 @@
+**/*_venv
+**/.idea
+*.log
+**/__pycache__
+**/.DS_Store
+**/out
+**/.vscode
+**/.pytest_cache
+**/*.egg*
+
+# recovery_config files
+recovery_config_*
+
+# file writer data
+**.h5
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/**/_build/
+docs/**/autodoc/
+docs/**/_autosummary/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+**.prof
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

bec_server-2.6.0/PKG-INFO

@@ -0,0 +1,32 @@
+Metadata-Version: 2.3
+Name: bec-server
+Version: 2.6.0
+Summary: BEC server
+Project-URL: Bug Tracker, https://gitlab.psi.ch/bec/bec/issues
+Project-URL: Homepage, https://gitlab.psi.ch/bec/bec
+Classifier: Development Status :: 3 - Alpha
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.10
+Requires-Dist: bec-lib
+Requires-Dist: cytoolz
+Requires-Dist: h5py
+Requires-Dist: libtmux
+Requires-Dist: lmfit
+Requires-Dist: msgpack
+Requires-Dist: numpy
+Requires-Dist: ophyd
+Requires-Dist: ophyd-devices
+Requires-Dist: py-scibec
+Requires-Dist: pydantic
+Requires-Dist: python-dotenv
+Requires-Dist: pyyaml
+Requires-Dist: rich
+Provides-Extra: dev
+Requires-Dist: black; extra == 'dev'
+Requires-Dist: coverage; extra == 'dev'
+Requires-Dist: isort; extra == 'dev'
+Requires-Dist: pylint; extra == 'dev'
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: pytest-random-order; extra == 'dev'
+Requires-Dist: pytest-timeout; extra == 'dev'

{bec-server-2.4.2 → bec_server-2.6.0}/bec_server/device_server/devices/devicemanager.py

@@ -13,7 +13,6 @@ from functools import reduce
 
 import numpy as np
 import ophyd
-import ophyd.sim as ops
 import ophyd_devices as opd
 from ophyd.ophydobj import OphydObject
 from ophyd.signal import EpicsSignalBase
@@ -27,16 +26,11 @@ from bec_lib import (
     MessageEndpoints,
     bec_logger,
     messages,
+    plugin_helper,
 )
 from bec_server.device_server.devices.config_update_handler import ConfigUpdateHandler
 from bec_server.device_server.devices.device_serializer import get_device_info
 
-try:
-    from bec_plugins import devices as plugin_devices
-except ImportError:
-    plugin_devices = None
-
-
 logger = bec_logger.logger
 
 
@@ -118,30 +112,8 @@ class DeviceManagerDS(DeviceManagerBase):
 
     @staticmethod
     def _get_device_class(dev_type: str) -> type:
-        """
-        Return the class object from 'dev_type' string in the form '[module:][submodule:]class_name'
-        The class is looked after in ophyd devices[.module][.submodule] first, if it is not
-        present plugin_devices, ophyd, ophyd_devices.sim are searched too
-
-        Args:
-            dev_type (str): device type string
-
-        Returns:
-            type: class object
-        """
-        submodule, _, class_name = dev_type.rpartition(":")
-        if submodule:
-            submodule = f".{submodule.replace(':', '.')}"
-        for parent_module in (opd, plugin_devices, ophyd, ops):
-            try:
-                module = __import__(f"{parent_module.__name__}{submodule}", fromlist=[""])
-            except ModuleNotFoundError:
-                continue
-            else:
-                break
-        else:
-            raise TypeError(f"Unknown device class {dev_type}")
-        return getattr(module, class_name)
+        """Get the device class from the device type"""
+        return plugin_helper.get_plugin_class(dev_type, [opd, ophyd])
 
     def _load_session(self, *_args, **_kwargs):
         delayed_init = []

{bec-server-2.4.2 → bec_server-2.6.0}/bec_server/file_writer/__init__.py

@@ -1,3 +1,3 @@
 from .cli.launch import main
-from .file_writer import NexusFileWriter, NeXusFileXMLWriter
+from .file_writer import NexusFileWriter
 from .file_writer_manager import FileWriterManager

{bec-server-2.4.2 → bec_server-2.6.0}/bec_server/file_writer/cli/launch.py

@@ -23,9 +23,6 @@ def main():
     config = ServiceConfig(config_path)
 
     file_writer_manager = file_writer.FileWriterManager(config, RedisConnector)
-    file_writer_manager.file_writer.configure(
-        layout_file=os.path.abspath("./layout_cSAXS_NXsas.xml")
-    )
     try:
         event = threading.Event()
         logger.success("Started FileWriter")

{bec-server-2.4.2 → bec_server-2.6.0}/bec_server/file_writer/file_writer.py

@@ -8,11 +8,10 @@ import traceback
 import typing
 
 import h5py
-import xmltodict
 
-import bec_server.file_writer_plugins as fwp
-from bec_lib import MessageEndpoints, bec_logger, messages
+from bec_lib import MessageEndpoints, bec_logger, messages, plugin_helper
 
+from .default_writer import NeXus_format as default_NeXus_format
 from .merged_dicts import merge_dicts
 
 logger = bec_logger.logger
@@ -49,107 +48,6 @@ class FileWriter(abc.ABC):
         return device_storage
 
 
-class XMLWriter:
-    @staticmethod
-    def get_type(type_string: str):
-        if type_string == "float":
-            return float
-        if type_string == "string":
-            return str
-        if type_string == "int":
-            return int
-        raise NeXusLayoutError(f"Unsupported data type {type_string}.")
-
-    def get_value(self, value, entry, source, data_type):
-        if source == "constant":
-            if data_type:
-                return self.get_type(data_type)(value)
-            return value
-        return entry
-
-    def add_group(self, container, val):
-        name = val.pop("@name")
-        group = container.create_group(name)
-        self.add_content(group, val)
-
-    def add_dataset(self, container, val):
-        name = val.pop("@name")
-        source = val.pop("@source")
-        value = val.pop("@value", None)
-        data_type = val.pop("@type", None)
-        entry = val.pop("@entry", None)
-
-        data = self.get_value(value=value, entry=entry, source=source, data_type=data_type)
-        if data is None:
-            return
-        dataset = container.create_dataset(name, data=data)
-        self.add_content(dataset, val)
-        return
-
-    def add_attribute(self, container, val):
-        name = val.pop("@name")
-        source = val.pop("@source")
-        value = val.pop("@value", None)
-        data_type = val.pop("@type", None)
-        entry = val.pop("@entry", None)
-
-        data = self.get_value(value=value, entry=entry, source=source, data_type=data_type)
-        setattr(container.attrs, name, data)
-
-    def add_hardlink(self, container, val):
-        pass
-
-    def add_softlink(self, container, val):
-        pass
-
-    def add_content(self, container, layout):
-        for key, values in layout.items():
-            if not isinstance(values, list):
-                values = [values]
-            for val in values:
-                if key == "group":
-                    self.add_group(container, val)
-                elif key == "hdf5_layout":
-                    self.add_base_entry(container, val)
-                elif key == "attribute":
-                    self.add_attribute(container, val)
-                elif key == "dataset":
-                    self.add_dataset(container, val)
-                elif key == "hardlink":
-                    self.add_hardlink(container, val)
-                elif key == "softlink":
-                    self.add_softlink(container, val)
-                else:
-                    pass
-                    # raise NeXusLayoutError()
-
-    def add_base_entry(self, container, val):
-        self.add_group(container, val["group"])
-
-
-class NeXusFileXMLWriter(FileWriter, XMLWriter):
-    def configure(self, layout_file, **kwargs):
-        self.layout_file = layout_file
-        with open(self.layout_file, "br") as f:
-            self.layout = xmltodict.parse(f)
-
-    def get_value(self, value, entry, source, data_type):
-        if source == "constant":
-            if data_type:
-                return self.get_type(data_type)(value)
-            return value
-        if source == "bec":
-            return self.data.get(entry)
-        return entry
-
-    def write(self, file_path: str, data):
-        print(f"writing file to {file_path}")
-        self.data = self._create_device_data_storage(data)
-
-        with h5py.File(file_path, "w") as file:
-            self.add_content(file, self.layout)
-
-
 class HDF5Storage:
     """
     The HDF5Storage class is a container used by the HDF5 writer plugins to store data in the correct NeXus format.
@@ -310,7 +208,16 @@ class NexusFileWriter(FileWriter):
             ).isoformat()
         if data.end_time is not None:
             device_storage["end_time"] = datetime.datetime.fromtimestamp(data.end_time).isoformat()
-        writer_format = getattr(fwp, self.file_writer_manager.file_writer_config.get("plugin"))
+
+        requested_plugin = self.file_writer_manager.file_writer_config.get("plugin")
+        if requested_plugin == "default_NeXus_format":
+            writer_format = default_NeXus_format
+        else:
+            plugins = plugin_helper.get_file_writer_plugins()
+            if requested_plugin not in plugins:
+                logger.error(f"Plugin {requested_plugin} not found. Using default plugin.")
+                writer_format = default_NeXus_format
+
         for file_ref in data.file_references.values():
             rel_path = os.path.relpath(file_ref["path"], os.path.dirname(file_path))
             file_ref["path"] = rel_path

bec_server-2.6.0/bec_server/file_writer_plugins/__init__.py

@@ -0,0 +1 @@
+from .cSAXS import NeXus_format as cSAXS_NeXus_format

{bec-server-2.4.2 → bec_server-2.6.0}/bec_server/scan_server/scan_manager.py

@@ -1,11 +1,6 @@
-import glob
-import importlib
-import importlib.util
 import inspect
-import os
-from pathlib import Path
 
-from bec_lib import MessageEndpoints, bec_logger
+from bec_lib import MessageEndpoints, bec_logger, plugin_helper
 from bec_lib.messages import AvailableResourceMessage
 from bec_lib.signature_serializer import signature_to_dict
 
@@ -15,7 +10,6 @@ logger = bec_logger.logger
 
 
 class ScanManager:
-    DEFAULT_PLUGIN_PATH = Path(os.path.dirname(os.path.abspath(__file__)) + "/../../").resolve()
 
     def __init__(self, *, parent):
         """
@@ -31,30 +25,17 @@ class ScanManager:
 
     def load_plugins(self):
         """load scan plugins"""
-        plugin_path = os.environ.get("BEC_PLUGIN_PATH")
-        if not plugin_path:
-            logger.info("BEC_PLUGIN_PATH not set. Using default plugin path.")
-            plugin_path = self.DEFAULT_PLUGIN_PATH
-        else:
-            logger.info(f"Using plugin path {plugin_path}")
-        plugin_path = os.path.join(plugin_path, "scan_server/scan_plugins")
-        files = glob.glob(os.path.join(plugin_path, "*.py"))
-        for file in files:
-            if file.endswith("__init__.py"):
+        plugins = plugin_helper.get_scan_plugins()
+        if not plugins:
+            return
+        for name, cls in plugins.items():
+            if not issubclass(cls, ScanServerScans.RequestBase):
+                logger.error(
+                    f"Plugin {name} is not a valid scan plugin as it does not inherit from RequestBase. Skipping."
+                )
                 continue
-            module_spec = importlib.util.spec_from_file_location("scan_plugins", file)
-            plugin_module = importlib.util.module_from_spec(module_spec)
-            module_spec.loader.exec_module(plugin_module)
-            module_members = inspect.getmembers(plugin_module)
-            for name, cls in module_members:
-                if not inspect.isclass(cls):
-                    continue
-                # ignore imported classes
-                if cls.__module__ != "scan_plugins":
-                    continue
-                if issubclass(cls, ScanServerScans.RequestBase):
-                    self._plugins[name] = cls
-                    logger.info(f"Loading scan plugin {name}")
+            self._plugins[name] = cls
+            logger.info(f"Loading scan plugin {name}")
 
     def update_available_scans(self):
         """load all scans and plugin scans"""

bec_server-2.6.0/pyproject.toml

@@ -0,0 +1,62 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "bec-server"
+version = "2.6.0"
+description = "BEC server"
+requires-python = ">=3.10"
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering",
+]
+dependencies = [
+    "bec-lib",
+    "cytoolz",
+    "h5py",
+    "libtmux",
+    "lmfit",
+    "msgpack",
+    "numpy",
+    "ophyd",
+    "ophyd_devices",
+    "pydantic",
+    "py-scibec",
+    "pyyaml",
+    "python-dotenv",
+    "rich",
+]
+
+[project.optional-dependencies]
+dev = [
+    "black",
+    "isort",
+    "coverage",
+    "pylint",
+    "pytest",
+    "pytest-random-order",
+    "pytest-timeout",
+]
+
+[project.scripts]
+bec-dap = "bec_server.data_processing:main"
+bec-device-server = "bec_server.device_server:main"
+bec-file-writer = "bec_server.file_writer:main"
+bec-scan-server = "bec_server.scan_server:main"
+bec-scan-bundler = "bec_server.scan_bundler:main"
+bec-scihub = "bec_server.scihub:main"
+bec-server = "bec_server:main"
+
+
+[project.urls]
+"Bug Tracker" = "https://gitlab.psi.ch/bec/bec/issues"
+Homepage = "https://gitlab.psi.ch/bec/bec"
+
+[tool.hatch.build.targets.wheel]
+include = ["*"]
+
+[tool.black]
+line-length = 100
+skip-magic-trailing-comma = true

bec_server-2.6.0/tests/tests_bec_server_utils/test_main.py

@@ -0,0 +1,68 @@
+from unittest import mock
+
+from bec_server.bec_server_utils.launch import main
+
+
+def test_main_start():
+    with mock.patch("bec_server.bec_server_utils.launch.ServiceHandler") as mock_service_handler:
+        with mock.patch("bec_server.bec_server_utils.launch.argparse") as mock_argparse:
+            mock_argparse.ArgumentParser().parse_args.return_value = mock.MagicMock(
+                command="start", config=None
+            )
+            main()
+            mock_service_handler.assert_called_once_with(
+                bec_path=mock.ANY, config_path=None, no_tmux=False
+            )
+            mock_service_handler().start.assert_called_once()
+
+
+def test_main_stop():
+    with mock.patch("bec_server.bec_server_utils.launch.ServiceHandler") as mock_service_handler:
+        with mock.patch("bec_server.bec_server_utils.launch.argparse") as mock_argparse:
+            mock_argparse.ArgumentParser().parse_args.return_value = mock.MagicMock(
+                command="stop", config=None
+            )
+            main()
+            mock_service_handler.assert_called_once_with(
+                bec_path=mock.ANY, config_path=None, no_tmux=False
+            )
+            mock_service_handler().stop.assert_called_once()
+
+
+def test_main_restart():
+    with mock.patch("bec_server.bec_server_utils.launch.ServiceHandler") as mock_service_handler:
+        with mock.patch("bec_server.bec_server_utils.launch.argparse") as mock_argparse:
+            mock_argparse.ArgumentParser().parse_args.return_value = mock.MagicMock(
+                command="restart", config=None
+            )
+            main()
+            mock_service_handler.assert_called_once_with(
+                bec_path=mock.ANY, config_path=None, no_tmux=False
+            )
+            mock_service_handler().restart.assert_called_once()
+
+
+def test_main_start_with_config():
+    with mock.patch("bec_server.bec_server_utils.launch.ServiceHandler") as mock_service_handler:
+        with mock.patch("bec_server.bec_server_utils.launch.argparse") as mock_argparse:
+            mock_argparse.ArgumentParser().parse_args.return_value = mock.MagicMock(
+                command="start", config="/path/to/config"
+            )
+            main()
+            mock_service_handler.assert_called_once_with(
+                bec_path=mock.ANY, config_path="/path/to/config", no_tmux=False
+            )
+            mock_service_handler().start.assert_called_once()
+
+
+def test_main_restart_with_config():
+    with mock.patch("bec_server.bec_server_utils.launch.ServiceHandler") as mock_service_handler:
+        with mock.patch("bec_server.bec_server_utils.launch.argparse") as mock_argparse:
+            mock_argparse.ArgumentParser().parse_args.return_value = mock.MagicMock(
+                command="restart", config="/path/to/config"
+            )
+            main()
+            mock_service_handler.assert_called_once_with(
+                bec_path=mock.ANY, config_path="/path/to/config", no_tmux=False
+            )
+            mock_service_handler().restart.assert_called_once()

bec_server-2.6.0/tests/tests_bec_server_utils/test_service_handler.py

@@ -0,0 +1,64 @@
+from unittest import mock
+
+from bec_server.bec_server_utils.service_handler import ServiceHandler
+
+
+def test_service_handler():
+    bec_path = "/path/to/bec"
+    config_path = "/path/to/config"
+
+    with mock.patch("bec_server.bec_server_utils.service_handler.sys") as mock_sys:
+        mock_sys.platform = "linux"
+        service_handler = ServiceHandler(bec_path, config_path)
+        assert service_handler.interface == "tmux"
+
+
+def test_service_handler_start():
+    bec_path = "/path/to/bec"
+    config_path = "/path/to/config"
+
+    with mock.patch("bec_server.bec_server_utils.service_handler.sys") as mock_sys:
+        mock_sys.platform = "linux"
+        service_handler = ServiceHandler(bec_path, config_path)
+
+        with mock.patch(
+            "bec_server.bec_server_utils.service_handler.tmux_start"
+        ) as mock_tmux_start:
+            service_handler.start()
+            mock_tmux_start.assert_called_once_with(bec_path, config_path, service_handler.SERVICES)
+
+
+def test_service_handler_stop():
+    with mock.patch("bec_server.bec_server_utils.service_handler.tmux_stop") as mock_tmux_stop:
+        service_handler = ServiceHandler("/path/to/bec", "/path/to/config")
+        service_handler.stop()
+        mock_tmux_stop.assert_called_once()
+
+
+def test_service_handler_restart():
+    bec_path = "/path/to/bec"
+    config_path = "/path/to/config"
+
+    with mock.patch("bec_server.bec_server_utils.service_handler.sys") as mock_sys:
+        mock_sys.platform = "linux"
+        service_handler = ServiceHandler(bec_path, config_path)
+
+        with mock.patch("bec_server.bec_server_utils.service_handler.tmux_stop") as mock_tmux_stop:
+            with mock.patch(
+                "bec_server.bec_server_utils.service_handler.tmux_start"
+            ) as mock_tmux_start:
+                service_handler.restart()
+                mock_tmux_stop.assert_called_once()
+                mock_tmux_start.assert_called_once_with(
+                    bec_path, config_path, service_handler.SERVICES
+                )
+
+
+def test_service_handler_services():
+    service_handler = ServiceHandler("/path/to/bec", "/path/to/config")
+    assert (
+        service_handler.SERVICES["scan_server"]["path"].substitute(base_path="/path/to/bec")
+        == "/path/to/bec/scan_server"
+    )
+
+    assert service_handler.SERVICES["scan_server"]["command"] == "bec-scan-server"