Merge pull request #103 from FAIRmat-NFDI/example-fix

fix example

CITATION.cff

@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 title: 'pynxtools-xps: A pynxtools reader plugin for X-ray photoelectron spectroscopy (XPS) data'
-version: 0.4.8
+version: 0.4.9
 message:
   If you use this software, please cite it using the
   metadata from this file.

src/pynxtools_xps/nomad/entrypoints.py

@@ -30,7 +30,7 @@
     description="""
         This example presents the capabilities of the NOMAD platform to store and standardize X-ray Photoelectron Spectroscopy XPS data.
         It shows the generation of a NeXus file according to the
-        [NXmpes](https://manual.nexusformat.org/classes/contributed_definitions/NXmpes.html#nxmpes)
+        [NXxps](https://fairmat-nfdi.github.io/nexus_definitions/classes/contributed_definitions/NXxps.html#nxxps)
         application definition from an example measurement file and a subseqeuent analysis of that data set.
     """,
     plugin_package="pynxtools_xps",

src/pynxtools_xps/nomad/examples/README.md

@@ -1,35 +1,35 @@
-# XPS Reader
+# Introduction
 
-## Introduction
+This example presents the capabilities of the NOMAD platform to store and standardize XPS data. It shows the generation of a NeXus file according to the [`NXxps`](https://fairmat-nfdi.github.io/nexus_definitions/classes/contributed_definitions/NXxps.html#nxxps) application definition and a successive analysis of an example data set.
 
-This example presents the capabilities of the NOMAD platform to store and standardize XPS data. It shows the generation of a NeXus file according to the [NXmpes](https://manual.nexusformat.org/classes/contributed_definitions/NXmpes.html#nxmpes) application definition and a successive analysis of an example data set.
-
-## Viewing uploaded data
+# Viewing uploaded data
 
 Below, you find an overview of your uploaded data.
-Click on the `> /` button to get a list of your data or select **FILES** from the top menu of this upload.
+Click on the `> /` button to get a list of your file or select **FILES** from the top menu of this upload.
+
+The general structure of this example is the following:
+- The starting point is the `xps.scheme.archive.yaml` file. This file defines a schema for the 
+electronic lab notebook (ELN) for XPS data. The ELN follows the general structure of NOMAD ELN templates and you may refer to the [documentation](https://nomad-lab.eu/prod/v1/staging/docs/archive.html) or a [YouTube tutorial](https://youtu.be/o5ETHmGmnaI) (~1h) for further information. This schema contains all the NeXus concepts that are defined in the `NXxps` application definition, but are not provided through the raw experimental file.
+Hence, these are the information that the user should enter.
+- The file `eln_conversion.archive.yaml` has two functionalities: 1) it implements the schema defined in `xps.scheme.archive.yaml` and prefills it with some values for this particular example, and 2) it uses the `ElnYamlConverter` from the NOMAD plugin [`pynxtools`](https://github.com/FAIRmat-NFDI/pynxtools) to convert the NOMAD ELN into a YAML file that can be used to populate the NeXus file.
+- In the next step, the `nexus_conversion.archive.json` is used to generate a NeXus file according to the `NXxps` application definition by calling the `NexusDataConverter` from `pynxtools`. It uses as input file the raw measurement file (`EX439_S718_Au_in_25_mbar_O2.sle`) as well as the newly generated `eln_data.yaml` to create the NeXus file `Au_25_mbar_O2_no_align.nxs`. You may view your supplied or generated NeXus files here with the H5Web viewer. To do so open the **FILES** tab and just select the `.nxs` file.
+- Finally, the `NexusParser` from `pynxtools` is called to read in the data in the NeXus file into the NOMAD metainfo. You can explore the parsed data in the **DATA** tab.
+
 You may add your own files to the upload or experiment with the pre-existing electronic lab notebook (ELN) example.
-The ELN follows the general structure of NOMAD ELN templates and you may refer to the [documentation](https://nomad-lab.eu/prod/v1/staging/docs/archive.html) or a [YouTube tutorial](https://youtu.be/o5ETHmGmnaI) (~1h)
-for further information.
-When the ELN is saved a NeXus file will be generated from the provided example data.
-You may also view your supplied or generated NeXus files here with the H5Web viewer.
-To do so open the **FILES** tab and just select a `.nxs` file.
 
-## Analyzing the data
+# Analyzing the data
 
 The examples work through the use of NOMAD remote tools hub (NORTH) containers, i.e. besides using and dealing with the uploaded XPS data, an analysis container can be started. If you want to execute the examples locally you may also use your local python and jupyterlab installation. Please refer to the documentation of [pynxtools](https://github.com/FAIRmat-NFDI/pynxtools.git) and [h5web](https://github.com/silx-kit/h5web) on how to install it on your machine.
 
-Note: To upload your own xps data file, you must check  **"eln_data.yaml"** file to provide all the required fields. In xps some required fields or attributes do not come with xps raw data. 
-
 To start an analysis, note your upload id (which you find on top of this explanation) and select **ANALYZE** from the top menu, then **NOMAD Remote Tools Hub**.
 In the appearing list you'll find the `xps` container, click on it and click **LAUNCH**.
 After a few moments a new tab will open which displays a jupyter environment providing the required analysis tools.
 To find the examples navigate to uploads inside the jupyter hub browser and select the folder with your noted upload id.
 There you'll find the example `ipynb` notebook for data analysis (E2).
 Double-clicking the notebook will open the example in the jupyter main window.
 
-## Where to go from here?
+# Where to go from here?
 
 If you're interested in using this pipeline and NOMAD in general you'll find support at [FAIRmat](https://www.fairmat-nfdi.eu/fairmat/consortium).
 
-For questions regarding the experiment or this specific example contact [Lukas Pielsticker](https://www.fairmat-nfdi.eu/fairmat/fairmat_/fairmatteam), [Rubel Mozumder](https://www.fairmat-nfdi.eu/fairmat/fairmat_/fairmatteam), or [Florian Dobener](https://www.fairmat-nfdi.eu/fairmat/fairmat_/fairmatteam).
+For questions regarding the experiment or this specific example contact [Lukas Pielsticker](https://www.fairmat-nfdi.eu/fairmat/fairmat_/fairmatteam) or the rest of the [FAIRmat team](https://www.fairmat-nfdi.eu/fairmat/fairmat_/fairmatteam).