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RubelMozumderRubelMozumder
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Uploading of the example files in nomad production successfully tested.
Separate upload script in script folder.
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‎pyproject.toml‎

Lines changed: 13 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -36,6 +36,8 @@ dependencies = [
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"Parent Project" = "https://github.com/FAIRmat-NFDI"
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[project.optional-dependencies]
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nomad = ["nomad-lab >= 1.4.0"]
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dev = [
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"mypy",
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"ruff>=0.14.0",
@@ -52,6 +54,11 @@ docs = [
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"mkdocs-simple-hooks",
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]
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nomad_api = [
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"requests",
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"nomad-lab >= 1.4.0",
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]
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[project.entry-points."pynxtools.reader"]
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spm = "pynxtools_spm.reader:SPMReader"
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@@ -70,7 +77,7 @@ version_scheme = "no-guess-dev"
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local_scheme = "node-and-date"
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[tool.ruff]
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include = ["src/pynxtools_spm/*.py", "tests/*.py"]
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include = ["src/pynxtools_spm/**/*.py", "tests/**/*.py"]
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lint.select = [
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"E", # pycodestyle
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"W", # pycodestyle
@@ -101,3 +108,8 @@ ignore_missing_imports = true
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follow_imports = "silent"
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no_strict_optional = true
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disable_error_code = "import, annotation-unchecked"
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[tool.uv]
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extra-index-url = [
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"https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple",
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]

‎scripts/example_upload_script.py‎

Lines changed: 134 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,134 @@
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from pynxtools_spm.nomad_uploader.uploader import (
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run_uploader_with,
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NOMADSettings,
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DataProcessingSettings,
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)
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from pathlib import Path
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current_dir = Path(__file__).resolve().parent
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project_dir = current_dir.parent
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nomad_settings = NOMADSettings(
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url_protocol="https",
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url_domain="nomad-lab.eu",
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url_version="prod/v1/develop/api/v1/",
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url="https://nomad-lab.eu/prod/v1/develop/api/v1/",
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username="",
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password="",
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token="",
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modify_upload_metadata=True,
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publish_to_nomad=False,
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)
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nanonis = project_dir / "tests/data/nanonis"
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total_upload = 3
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data_proc_settings = DataProcessingSettings(
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raw_file_exts=(
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".dat",
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".sxm",
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),
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single_batch_processing_time=total_upload * 90, # seconds
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src_dir=nanonis,
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# copy_file_elsewhere=False,
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dst_dir="",
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create_pseudo_file=True,
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pseudo_exts=".done",
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spm_params_obj_l=[],
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sts_eln=nanonis / "sts/version_gen_5e_with_described_nxdata/eln_data.yaml",
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sts_config="",
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stm_eln=nanonis / "stm/version_gen_5_with_described_nxdata/eln_data.yaml",
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stm_config="",
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afm_eln=nanonis / "afm/version_gen_4_with_described_nxdata/eln_data.yaml",
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afm_config="",
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logger_dir=current_dir,
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number_of_uploads=total_upload,
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file_to_convert_data={
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f"{nanonis / 'stm/version_gen_5_with_described_nxdata/Au_mica_2023_Y_A_diPAMY_195.sxm'}": {
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"eln": "",
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"technique": "stm",
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},
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f"{nanonis / 'sts/version_gen_5e_with_described_nxdata/STS_nanonis_generic_5e_1.dat'}": {
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"eln": "",
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"technique": "sts",
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},
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f"{nanonis / 'stm/version_gen_5_with_described_nxdata/Au_mica_2023_Y_A_diPAMY_195.sxm'}": {
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"eln": "",
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"technique": "stm",
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},
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f"{nanonis / 'sts/version_gen_5e_with_described_nxdata/STS_nanonis_generic_5e_1.dat'}": {
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"eln": "",
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"technique": "sts",
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},
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f"{nanonis / 'stm/version_gen_5_with_described_nxdata/Au_mica_2023_Y_A_diPAMY_195.sxm'}": {
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"eln": "",
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"technique": "stm",
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},
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f"{nanonis / 'sts/version_gen_5e_with_described_nxdata/STS_nanonis_generic_5e_1.dat'}": {
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"eln": "",
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"technique": "sts",
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},
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f"{nanonis / 'stm/version_gen_5_with_described_nxdata/Au_mica_2023_Y_A_diPAMY_195.sxm'}": {
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"eln": "",
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"technique": "stm",
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},
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f"{nanonis / 'sts/version_gen_5e_with_described_nxdata/STS_nanonis_generic_5e_1.dat'}": {
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"eln": "",
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"technique": "sts",
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},
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f"{nanonis / 'stm/version_gen_5_with_described_nxdata/Au_mica_2023_Y_A_diPAMY_195.sxm'}": {
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"eln": "",
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"technique": "stm",
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},
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f"{nanonis / 'sts/version_gen_5e_with_described_nxdata/STS_nanonis_generic_5e_1.dat'}": {
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"eln": "",
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"technique": "sts",
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},
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f"{nanonis / 'stm/version_gen_5_with_described_nxdata/Au_mica_2023_Y_A_diPAMY_195.sxm'}": {
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"eln": "",
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"technique": "stm",
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},
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f"{nanonis / 'sts/version_gen_5e_with_described_nxdata/STS_nanonis_generic_5e_1.dat'}": {
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"eln": "",
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"technique": "sts",
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},
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f"{nanonis / 'stm/version_gen_5_with_described_nxdata/Au_mica_2023_Y_A_diPAMY_195.sxm'}": {
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"eln": "",
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"technique": "stm",
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},
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f"{nanonis / 'sts/version_gen_5e_with_described_nxdata/STS_nanonis_generic_5e_1.dat'}": {
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"eln": "",
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"technique": "sts",
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},
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f"{nanonis / 'stm/version_gen_5_with_described_nxdata/Au_mica_2023_Y_A_diPAMY_195.sxm'}": {
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"eln": "",
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"technique": "stm",
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},
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f"{nanonis / 'sts/version_gen_5e_with_described_nxdata/STS_nanonis_generic_5e_1.dat'}": {
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"eln": "",
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"technique": "sts",
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},
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},
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# metadata = {
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# "metadata": {
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# "upload_name": upload_name,
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# "references": ["https://doi.org/xx.xxxx/xxxxxx"],
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# "datasets": dataset_id,
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# "embargo_length": 0,
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# "coauthors": ["coauthor@affiliation.de"],
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# "comment": 'This is a test upload...'
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# },
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# }
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upload_metadata={
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"metadata": {
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"coauthors": ["cojaddl@physik.hu-berlin.de"],
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"upload_name": "test_upload",
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}
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},
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)
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if __name__ == "__main__":
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run_uploader_with(
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nomad_settings=nomad_settings,
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data_proc_settings=data_proc_settings,
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)

run_uploader.sh renamed to scripts/run_uploader.sh

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -3,9 +3,10 @@
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# Stop on error
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set -e
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6-
current_dir=$(pwd)
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uploader_script="/home/rubel/NOMAD-FAIRmat/nomad-distro-dev-RM/packages/pynxtools-spm/src/pynxtools_spm/nomad_uploader/example_upload_script.py"
8-
venv="/home/rubel/NOMAD-FAIRmat/nomad-distro-dev-RM/.venv"
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current_dir=$(dirname $(realpath $0))
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echo "Current directory: $current_dir"
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uploader_script="$current_dir/example_upload_script.py"
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venv="/home/rubel/NOMAD-FAIRmat/GH/pynxtools-spm/.venv"
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python_3="$venv/bin/python3"
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echo "Running uploader script..."
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"$python_3" "$uploader_script" > "$current_dir/debug.txt" 2>&1

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