Example upload task

.cspell/custom-dictionary.txt

@@ -104,3 +104,6 @@ ureg
 valinit
 valtext
 Yichen
+pynx
+zipf
+arcname

README.md

@@ -10,8 +10,6 @@
 
 # `pynxtools-spm`: A `pynxtools` reader for SPM data
 
-.
-
 This `pynxtools` plugin was generated with [`cookiecutter`](https://github.com/cookiecutter/cookiecutter) using the [`pynxtools-plugin-template`](https://github.com/FAIRmat-NFDI/`pynxtools-plugin-template) template.
 
 ## Installation
@@ -37,4 +35,4 @@ More information about this pynxtools plugin is available in the [documentation]
 Rubel Mozumder
 
 
-**Note**: This repository is an upgraded and renamed version of [pynxtools-stm](https://github.com/FAIRmat-NFDI/pynxtools-stm), which is now archived. In addition to the integration of new readers (e.g., `AFM`), all functionalities of `pynxtools-stm` remain available in this repository.
+**Note**: This repository is an upgraded and renamed version of [pynxtools-stm](https://github.com/FAIRmat-NFDI/pynxtools-stm), which is now archived. In addition to the integration of new readers (e.g., `AFM`), all functionalities of `pynxtools-stm` remain available in this repository.

pyproject.toml

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

scripts/example_upload_script.py

@@ -0,0 +1,134 @@
+from pynxtools_spm.nomad_uploader.uploader import (
+    run_uploader_with,
+    NOMADSettings,
+    DataProcessingSettings,
+)
+from pathlib import Path
+
+current_dir = Path(__file__).resolve().parent
+project_dir = current_dir.parent
+
+nomad_settings = NOMADSettings(
+    url_protocol="https",
+    url_domain="nomad-lab.eu",
+    url_version="prod/v1/develop/api/v1/",
+    url="https://nomad-lab.eu/prod/v1/develop/api/v1/",
+    username="Mozumder",
+    password="*#R516660a*#",
+    token="",
+    modify_upload_metadata=True,
+    publish_to_nomad=False,
+)
+nanonis = project_dir / "tests/data/nanonis"
+
+total_upload = 3
+
+data_proc_settings = DataProcessingSettings(
+    raw_file_exts=(
+        ".dat",
+        ".sxm",
+    ),
+    single_batch_processing_time=total_upload * 90,  # seconds
+    src_dir=nanonis,
+    # copy_file_elsewhere=False,
+    dst_dir="",
+    create_pseudo_file=True,
+    pseudo_exts=".done",
+    spm_params_obj_l=[],
+    sts_eln=nanonis / "sts/version_gen_5e_with_described_nxdata/eln_data.yaml",
+    sts_config="",
+    stm_eln=nanonis / "stm/version_gen_5_with_described_nxdata/eln_data.yaml",
+    stm_config="",
+    afm_eln=nanonis / "afm/version_gen_4_with_described_nxdata/eln_data.yaml",
+    afm_config="",
+    logger_dir=current_dir,
+    number_of_uploads=total_upload,
+    file_to_convert_data={
+        f"{nanonis / 'stm/version_gen_5_with_described_nxdata/Au_mica_2023_Y_A_diPAMY_195.sxm'}": {
+            "eln": "",
+            "technique": "stm",
+        },
+        f"{nanonis / 'sts/version_gen_5e_with_described_nxdata/STS_nanonis_generic_5e_1.dat'}": {
+            "eln": "",
+            "technique": "sts",
+        },
+        f"{nanonis / 'stm/version_gen_5_with_described_nxdata/Au_mica_2023_Y_A_diPAMY_195.sxm'}": {
+            "eln": "",
+            "technique": "stm",
+        },
+        f"{nanonis / 'sts/version_gen_5e_with_described_nxdata/STS_nanonis_generic_5e_1.dat'}": {
+            "eln": "",
+            "technique": "sts",
+        },
+        f"{nanonis / 'stm/version_gen_5_with_described_nxdata/Au_mica_2023_Y_A_diPAMY_195.sxm'}": {
+            "eln": "",
+            "technique": "stm",
+        },
+        f"{nanonis / 'sts/version_gen_5e_with_described_nxdata/STS_nanonis_generic_5e_1.dat'}": {
+            "eln": "",
+            "technique": "sts",
+        },
+        f"{nanonis / 'stm/version_gen_5_with_described_nxdata/Au_mica_2023_Y_A_diPAMY_195.sxm'}": {
+            "eln": "",
+            "technique": "stm",
+        },
+        f"{nanonis / 'sts/version_gen_5e_with_described_nxdata/STS_nanonis_generic_5e_1.dat'}": {
+            "eln": "",
+            "technique": "sts",
+        },
+        f"{nanonis / 'stm/version_gen_5_with_described_nxdata/Au_mica_2023_Y_A_diPAMY_195.sxm'}": {
+            "eln": "",
+            "technique": "stm",
+        },
+        f"{nanonis / 'sts/version_gen_5e_with_described_nxdata/STS_nanonis_generic_5e_1.dat'}": {
+            "eln": "",
+            "technique": "sts",
+        },
+        f"{nanonis / 'stm/version_gen_5_with_described_nxdata/Au_mica_2023_Y_A_diPAMY_195.sxm'}": {
+            "eln": "",
+            "technique": "stm",
+        },
+        f"{nanonis / 'sts/version_gen_5e_with_described_nxdata/STS_nanonis_generic_5e_1.dat'}": {
+            "eln": "",
+            "technique": "sts",
+        },
+        f"{nanonis / 'stm/version_gen_5_with_described_nxdata/Au_mica_2023_Y_A_diPAMY_195.sxm'}": {
+            "eln": "",
+            "technique": "stm",
+        },
+        f"{nanonis / 'sts/version_gen_5e_with_described_nxdata/STS_nanonis_generic_5e_1.dat'}": {
+            "eln": "",
+            "technique": "sts",
+        },
+        f"{nanonis / 'stm/version_gen_5_with_described_nxdata/Au_mica_2023_Y_A_diPAMY_195.sxm'}": {
+            "eln": "",
+            "technique": "stm",
+        },
+        f"{nanonis / 'sts/version_gen_5e_with_described_nxdata/STS_nanonis_generic_5e_1.dat'}": {
+            "eln": "",
+            "technique": "sts",
+        },
+    },
+    #     metadata = {
+    #     "metadata": {
+    #     "upload_name": upload_name,
+    #     "references": ["https://doi.org/xx.xxxx/xxxxxx"],
+    #     "datasets": dataset_id,
+    #     "embargo_length": 0,
+    #     "coauthors": ["coauthor@affiliation.de"],
+    #     "comment": 'This is a test upload...'
+    #     },
+    # }
+    upload_metadata={
+        "metadata": {
+            "coauthors": ["cojaddl@physik.hu-berlin.de"],
+            "upload_name": "test_upload",
+        }
+    },
+)
+
+if __name__ == "__main__":
+    run_uploader_with(
+        nomad_settings=nomad_settings,
+        data_proc_settings=data_proc_settings,
+    )

scripts/run_uploader.sh

@@ -0,0 +1,13 @@
+#! /bin/bash
+
+# Stop on error
+set -e
+
+current_dir=$(dirname $(realpath $0))
+echo "Current directory: $current_dir"
+uploader_script="$current_dir/example_upload_script.py"
+venv="/home/rubel/NOMAD-FAIRmat/GH/pynxtools-spm/.venv"
+python_3="$venv/bin/python3"
+echo "Running uploader script..."
+"$python_3" "$uploader_script" > "$current_dir/debug.txt" 2>&1
+echo "Uploader script finished. Check debug.txt for details."