Full update opencode big pickle

.env

@@ -0,0 +1,2 @@
+PREFECT_LOGGING_EXTRA_LOGGERS=bluesky_tiled_plugins.validator
+TILED_RETRY_ATTEMPTS=3

.gitignore

@@ -8,7 +8,6 @@ __pycache__/
 
 # Distribution / packaging
 .Python
-env/
 build/
 develop-eggs/
 dist/
@@ -20,10 +19,12 @@ lib64/
 parts/
 sdist/
 var/
-venv/
+wheels/
+share/python-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
+MANIFEST
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -38,31 +39,139 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
+.nox/
 .coverage
 .coverage.*
 .cache
 nosetests.xml
 coverage.xml
-*,cover
+*.cover
+*.py,cover
 .hypothesis/
+.pytest_cache/
+cover/
 
 # Translations
 *.mo
 *.pot
 
 # Django stuff:
 *.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
 
-# Sphinx documentation
-docs/build/
-docs/source/generated/
+# Flask stuff:
+instance/
+.webassets-cache
 
-# pytest
-.pytest_cache/
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
 
 # PyBuilder
+.pybuilder/
 target/
 
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# 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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.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/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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
+.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/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
 # Editor files
 #mac
 .DS_Store
@@ -78,9 +187,6 @@ target/
 #vscode
 .vscode/*
 
-#Ipython Notebook
-.ipynb_checkpoints
-
 #file extensions
 #
 *.h5

Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/prefix-dev/pixi:0.57.0
+FROM ghcr.io/prefix-dev/pixi:0.71.3
 
 ENV TZ="America/New_York"
 
@@ -7,6 +7,7 @@ RUN apt-get -y update && \
 
 COPY pixi.toml .
 COPY pixi.lock .
+COPY .env .
 # use `--locked` to ensure the lockfile is up to date with pixi.toml
 RUN pixi install --locked
 # create the shell-hook bash script to activate the environment

data_validation.py

@@ -1,28 +1,56 @@
-import time
+import os
+import time as ttime
 
+from dotenv import load_dotenv
 from prefect import flow, get_run_logger, task
-from export_tools import initialize_tiled_client
+from tiled.client import from_uri
+
+BEAMLINE_OR_ENDSTATION = "ucal"
+
+
+def get_api_key_from_env():
+    with open("/srv/container.secret", "r") as secrets:
+        load_dotenv(stream=secrets)
+    api_key = os.environ["TILED_API_KEY"]
+    return api_key
 
 
 @task(retries=2, retry_delay_seconds=10)
-def read_all_streams(uid, beamline_acronym="ucal"):
-    logger = get_run_logger()
-    catalog = initialize_tiled_client(beamline_acronym)
-    run = catalog[uid]
+def get_catalog(api_key=None):
+    if not api_key:
+        api_key = get_api_key_from_env()
+    catalog = from_uri("https://tiled.nsls2.bnl.gov", api_key=api_key)[
+        f"{BEAMLINE_OR_ENDSTATION}/raw"
+    ]
+    return catalog
+
+
+@task(retries=2, retry_delay_seconds=10)
+def get_run(uid, api_key=None):
+    if not api_key:
+        api_key = get_api_key_from_env()
+    cl = from_uri("https://tiled.nsls2.bnl.gov", api_key=api_key)
+    run = cl[f"{BEAMLINE_OR_ENDSTATION}/raw"][uid]
+    return run
+
 
-    logger.info(f"Validating uid {run.start['uid']}")
-    start_time = time.monotonic()
-    for stream in run:
+@task(retries=2, retry_delay_seconds=10)
+def read_stream(run, stream):
+    return run[stream].read()
+
+
+@flow
+def data_validation(uid, api_key=None, dry_run=False):
+    logger = get_run_logger()
+    logger.info(f"Validating uid {uid}")
+    start_time = ttime.monotonic()
+    run_client = get_run(uid, api_key=api_key)
+    for stream in run_client:
         logger.info(f"{stream}:")
-        stream_start_time = time.monotonic()
-        stream_data = run[stream].read()
-        stream_elapsed_time = time.monotonic() - stream_start_time
+        stream_start_time = ttime.monotonic()
+        stream_data = read_stream(run_client, stream)  # noqa: F841
+        stream_elapsed_time = ttime.monotonic() - stream_start_time
         logger.info(f"{stream} elapsed_time = {stream_elapsed_time}")
         logger.info(f"{stream} nbytes = {stream_data.nbytes:_}")
-    elapsed_time = time.monotonic() - start_time
+    elapsed_time = ttime.monotonic() - start_time
     logger.info(f"{elapsed_time = }")
-
-
-@flow
-def general_data_validation(uid, beamline_acronym="ucal"):
-    read_all_streams(uid, beamline_acronym)

end_of_run_export.py

@@ -3,7 +3,8 @@
 import os
 from export_to_xdi import exportToXDI
 from export_to_hdf5 import exportToHDF5
-from export_tools import get_proposal_path, initialize_tiled_client
+from data_validation import get_run
+from export_tools import get_proposal_path
 import datetime
 
 
@@ -28,28 +29,35 @@ def create_export_path(export_path):
 
 
 @task(retries=2, retry_delay_seconds=10)
-def export_all_streams(uid, beamline_acronym="ucal"):
+def export_all_streams(uid, api_key=None, dry_run=False):
     logger = get_run_logger()
-    catalog = initialize_tiled_client(beamline_acronym)
-    run = catalog[uid]
+    run = get_run(uid, api_key=api_key)
 
     base_export_path = get_export_path(run)
     logger.info(f"Generating Export for uid {run.start['uid']}")
     logger.info(f"Export Data to {base_export_path}")
-    create_export_path(base_export_path)
+    if not dry_run:
+        create_export_path(base_export_path)
 
     logger.info("Exporting XDI")
     xdi_export_path = join(base_export_path, "xdi")
-    create_export_path(xdi_export_path)
-    exportToXDI(xdi_export_path, run)
+    if not dry_run:
+        create_export_path(xdi_export_path)
+        exportToXDI(xdi_export_path, run)
+    else:
+        logger.info(f"dry_run: not exporting to {xdi_export_path}")
     logger.info("Exporting HDF5")
     hdf5_export_path = join(base_export_path, "hdf5")
-    create_export_path(hdf5_export_path)
-    exportToHDF5(hdf5_export_path, run)
+    if not dry_run:
+        create_export_path(hdf5_export_path)
+        exportToHDF5(hdf5_export_path, run)
+    else:
+        logger.info(f"dry_run: not exporting to {hdf5_export_path}")
     # logger.info("Exporting Athena")
+    # if not dry_run:
     # exportToAthena(export_path, run)
 
 
 @flow
-def general_data_export(uid, beamline_acronym="ucal"):
-    export_all_streams(uid, beamline_acronym)
+def general_data_export(uid, api_key=None, dry_run=False):
+    export_all_streams(uid, api_key=api_key, dry_run=dry_run)