From 0c02e16fbebd7f00d0d3614cc20995a51eb18fe9 Mon Sep 17 00:00:00 2001 From: temok-mx <temok.mx@gmail.com> Date: Thu, 10 Sep 2020 17:23:12 +0200 Subject: [PATCH] Updated README.md; added metadata.yml; the lead branch is now master, inactive branches became tags --- README.md | 85 ++++++++++++++++++++++++++++++++++++++++++++-------- metadata.yml | 8 +++++ 2 files changed, 80 insertions(+), 13 deletions(-) create mode 100644 metadata.yml diff --git a/README.md b/README.md index 8fd10f6..4146bde 100644 --- a/README.md +++ b/README.md @@ -1,19 +1,78 @@ -# mpesparser -@author = R. Patrick Xian (xian@fhi-berlin.mpg.de) +This is a NOMAD parser for [MPES](https://mpes-kit.github.io/mpes). It will read MPES input and +output files and provide all information in NOMAD's unified Metainfo based Archive format. -## About +## Preparing code input and output file for uploading to NOMAD -Multidimensional photoemission spectroscopy (MPES) experimental data parser for NOMAD-FAIR database. +NOMAD accepts `.zip` and `.tar.gz` archives as uploads. Each upload can contain arbitrary +files and directories. NOMAD will automatically try to choose the right parser for you files. +For each parser (i.e. for each supported code) there is one type of file that the respective +parser can recognize. We call these files `mainfiles` as they typically are the main +output file a code. For each `mainfile` that NOMAD discovers it will create an entry +in the database that users can search, view, and download. NOMAD will associate all files +in the same directory as files that also belong to that entry. Parsers +might also read information from these auxillary files. This way you can add more files +to an entry, even if the respective parser/code might not directly support it. -## Description of files -The set of important files for the parser are explained in the following, -- [mpesparser](mpesparser): Main folder of the parser. -- [mpesparser/__init__.py](mpesparser/__init__.py): Parser module initialization code. -- [mpesparser/__main__.py](mpesparser/__main__.py): Parser module run file. -- [mpesparser/mpes.nomadmetainfo.json](mpesparser/mpes.nomadmetainfo.json): MPES metadata definitions. +For mpes please provide at least the files from this table if applicable to your +calculations (remember that you can provide more files if you want): -To run the parser: + + +To create an upload with all calculations in a directory structure: + +``` +zip -r <upload-file>.zip <directory>/* +``` + +Go to the [NOMAD upload page](https://nomad-lab.eu/prod/rae/gui/uploads) to upload files +or find instructions about how to upload files from the command line. + +## Using the parser + +You can use NOMAD's parsers and normalizers locally on your computer. You need to install +NOMAD's pypi package: + +``` +pip install nomad-lab +``` + +To parse code input/output from the command line, you can use NOMAD's command line +interface (CLI) and print the processing results output to stdout: + +``` +nomad parse --show-archive <path-to-file> ``` -cd nomad/dependencies/parsers/parser-mpes -python -m parser-mpes tests/mpes.metadata_redacted.json + +To parse a file in Python, you can program something like this: +```python +import sys +from nomad.cli.parse import parse, normalize_all + +# match and run the parser +backend = parse(sys.argv[1]) +# run all normalizers +normalize_all(backend) + +# get the 'main section' section_run as a metainfo object +section_run = backend.resource.contents[0].section_run[0] + +# get the same data as JSON serializable Python dict +python_dict = section_run.m_to_dict() +``` + +## Developing the parser + +Also install NOMAD's pypi package: + +``` +pip install nomad-lab ``` + +Clone the parser project and install it in development mode: + +``` +git clone https://gitlab.mpcdf.mpg.de/nomad-lab/parser-mpes parser-mpes +pip install -e parser-mpes +``` + +Running the parser now, will use the parser's Python code from the clone project. diff --git a/metadata.yml b/metadata.yml new file mode 100644 index 0000000..3bdf208 --- /dev/null +++ b/metadata.yml @@ -0,0 +1,8 @@ +code-label: MPES +code-label-style: All in capitals +code-url: https://mpes-kit.github.io/mpes +parser-dir-name: dependencies/parsers/mpes/ +parser-git-url: https://gitlab.mpcdf.mpg.de/nomad-lab/parser-mpes +parser-specific: | + MPES (Multidimensional photoemission spectroscopy) is a parser for experimental data. +table-of-files: '' -- GitLab