From d935d9df033c52980a912ac5a44e820faa5511ac Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Tue, 12 May 2026 17:20:32 -0400 Subject: [PATCH 1/5] fix bad url in link --- end_of_run_workflow.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/end_of_run_workflow.py b/end_of_run_workflow.py index c1b8e93..67c244d 100644 --- a/end_of_run_workflow.py +++ b/end_of_run_workflow.py @@ -77,7 +77,7 @@ def end_of_run_workflow(stop_doc, api_key=None, dry_run=False): flow_run = FlowRunContext.get().flow_run # Add link to flow-run for the message to mon-prefect-im. program_message = ( - f":bangbang: {CATALOG_NAME} flow-run failed. (*{flow_run_name}*)\n ```run_start: {uid}\nscan_id: {scan_id}``` ```{tb[-1]}```" ) mon_prefect_im.notify(program_message) From c203c354a27e036d73e354129c3441a57bf1ec73 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 13 May 2026 07:49:53 -0400 Subject: [PATCH 2/5] fix api key handling * move API key handling from environment to get_run * clean up code related to getting API key from env outside of get_run() --- data_validation.py | 14 +++++++++++++- end_of_run_workflow.py | 11 ----------- 2 files changed, 13 insertions(+), 12 deletions(-) diff --git a/data_validation.py b/data_validation.py index 549278a..9aed2f6 100644 --- a/data_validation.py +++ b/data_validation.py @@ -1,10 +1,22 @@ -from prefect import task, flow, get_run_logger +import os import time as ttime + +from prefect import task, flow, get_run_logger from tiled.client import from_uri +from dotenv import load_dotenv + + +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 def get_run(uid, api_key=None): + if not api_key: + api_key = get_api_key_from_env() tiled_client = from_uri("https://tiled.nsls2.bnl.gov", api_key=api_key) run = tiled_client["srx/raw"][uid] return run diff --git a/end_of_run_workflow.py b/end_of_run_workflow.py index 67c244d..ec754ea 100644 --- a/end_of_run_workflow.py +++ b/end_of_run_workflow.py @@ -16,13 +16,6 @@ CATALOG_NAME = "srx" -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 - - def slack(func): """ Send a message to mon-prefect and mon-prefect-im slack channels if the flow-run failed. @@ -46,10 +39,6 @@ def end_of_run_workflow(stop_doc, api_key=None, dry_run=False): # Get the uid. uid = stop_doc["run_start"] - # Get Tiled API key, if not set already - if not api_key: - api_key = get_api_key_from_env() - # Get the scan_id. run = get_run(uid, api_key=api_key) scan_id = run.start["scan_id"] From 14a1c533e8a11e06299ba38609cec9dd69e7c2b0 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 13 May 2026 08:04:58 -0400 Subject: [PATCH 3/5] add python-dotenv to pixi.toml --- pixi.lock | 19 +++++++++---------- pixi.toml | 1 + 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/pixi.lock b/pixi.lock index f17639a..926dacd 100644 --- a/pixi.lock +++ b/pixi.lock @@ -289,7 +289,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/python-3.12.11-h9e4cc4f_0_cpython.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/python-blosc2-3.12.2-py312h8dbdb60_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0.post0-pyhe01879c_2.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.1.1-pyhe01879c_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-graphviz-0.21-pyhbacfb6d_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-multipart-0.0.20-pyhff2d567_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-slugify-8.0.4-pyhd8ed1ab_1.conda @@ -676,7 +676,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/osx-64/python-3.12.12-h3999593_0_cpython.conda - conda: https://conda.anaconda.org/conda-forge/osx-64/python-blosc2-3.12.2-py312hb880408_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0.post0-pyhe01879c_2.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.1.1-pyhe01879c_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-graphviz-0.21-pyhbacfb6d_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-multipart-0.0.20-pyhff2d567_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-slugify-8.0.4-pyhd8ed1ab_1.conda @@ -1046,7 +1046,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/osx-arm64/python-3.12.12-hec0b533_0_cpython.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/python-blosc2-3.12.2-py312hb52615a_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0.post0-pyhe01879c_2.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.1.1-pyhe01879c_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-graphviz-0.21-pyhbacfb6d_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-multipart-0.0.20-pyhff2d567_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/python-slugify-8.0.4-pyhd8ed1ab_1.conda @@ -10574,18 +10574,17 @@ packages: - pkg:pypi/python-dateutil?source=hash-mapping size: 233310 timestamp: 1751104122689 -- conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.1.1-pyhe01879c_0.conda - sha256: 9a90570085bedf4c6514bcd575456652c47918ff3d7b383349e26192a4805cc8 - md5: a245b3c04afa11e2e52a0db91550da7c +- conda: https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda + sha256: 74e417a768f59f02a242c25e7db0aa796627b5bc8c818863b57786072aeb85e5 + md5: 130584ad9f3a513cdd71b1fdc1244e9c depends: - - python >=3.9 - - python + - python >=3.10 license: BSD-3-Clause license_family: BSD purls: - pkg:pypi/python-dotenv?source=hash-mapping - size: 26031 - timestamp: 1750789290754 + size: 27848 + timestamp: 1772388605021 - conda: https://conda.anaconda.org/conda-forge/noarch/python-graphviz-0.21-pyhbacfb6d_0.conda sha256: b0139f80dea17136451975e4c0fefb5c86893d8b7bc6360626e8b025b8d8003a md5: 606d94da4566aa177df7615d68b29176 diff --git a/pixi.toml b/pixi.toml index 40178af..217e01a 100644 --- a/pixi.toml +++ b/pixi.toml @@ -13,6 +13,7 @@ scikit-beam = "*" pre-commit = ">=4.3.0,<5" databroker = "*" pillow = ">=12.2.0,<13" +python-dotenv = ">=1.2.2,<2" [pypi-dependencies] pyxrf = { git = "https://github.com/NSLS2/pyxrf.git", rev="7b7d868" } From b2fcec7ddb6133f1ca8cd64799a9aa25ea2d2898 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 13 May 2026 08:05:54 -0400 Subject: [PATCH 4/5] pre-commit lint --- end_of_run_workflow.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/end_of_run_workflow.py b/end_of_run_workflow.py index ec754ea..c2870cb 100644 --- a/end_of_run_workflow.py +++ b/end_of_run_workflow.py @@ -9,8 +9,6 @@ from xrf_hdf5_exporter import xrf_hdf5_exporter from vlm_snapshot_exporter import vlm_image_exporter from logscan import logscan -from dotenv import load_dotenv -import os from data_validation import get_run CATALOG_NAME = "srx" From 284cbaf8708df91fcce88122a4a955193f3a3c92 Mon Sep 17 00:00:00 2001 From: Jun Aishima Date: Wed, 13 May 2026 11:21:54 -0400 Subject: [PATCH 5/5] update pixi lock file --- pixi.lock | 14654 +++++++++++++++++++++++++++++----------------------- 1 file changed, 8206 insertions(+), 6448 deletions(-) diff --git a/pixi.lock b/pixi.lock index 926dacd..8dd0a76 100644 --- a/pixi.lock +++ b/pixi.lock @@ -7,1194 +7,1552 @@ environments: - 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