imas-data-dictionary


Nameimas-data-dictionary JSON
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SummaryThe Data Dictionary is the implementation of the Data Model of ITER's Integrated Modelling & Analysis Suite (IMAS)
upload_time2025-01-30 11:49:10
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licenseCopyright (c) 2012-2023, ITER Organization, Route de Vinon-sur-Verdon, CS 90 046, 13067 St-Paul-lez-Durance Cedex, France All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Use and redistribution, for peaceful purposes only, are granted solely to the ITER Members (the People's Republic of China, the European Atomic Energy Community, the Republic of India, Japan, the Republic of Korea, the Russian Federation, and the United States of America), with the right to sub-license within their territory for the purpose of fusion research and development. Organizations, bodies or individuals of non-ITER Members shall seek specific written permission from the ITER Organization before use or redistribution of this software. * All modifications/derivatives shall be made available to the ITER Organization. * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the ITER Organization nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE ITER ORGANIZATION OR ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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            # IMAS Data Dictionary

The Data Dictionary is the implementation of the Data Model of ITER's
Integrated Modelling & Analysis Suite (IMAS). It describes the
structuring and naming of data (as a set of Interface Data Structures
or IDSs) being used for both simulated and experimental data in a
machine agnostic manner.

IDSs are used for standardizing data representation, facilitating
exploration and comparison, as well as for standardizing coupling
interfaces between codes in an Integrated Modelling workflow. The Data
Dictionary itself does not describe explicitly how the data will be
stored on disk but is used at compile time or at runtime by various
pieces of data access software (e.g. the
[Access-Layer](https://git.iter.org/projects/IMAS/repos/access-layer)
which handle data archiving and retrieval within applications.

IDSs of the Data Dictionary follow a strict lifecycle that aims at
controlling the compatibility between various releases. This lifecycle
is fully described in the following external document:
[ITER_D_QQYMUK](https://user.iter.org/?uid=QQYMUK).

As it is generic and machine agnostic by design, the IMAS Data Model,
and by extension its implementation as the Data Dictionary, have the
potential to serve as a data standard for the fusion community. As
such, it benefits from the wide involvement of specialists and active
users and developers in the various areas being described. If you want
to contribute to the improvement of the Data Dictionary, either as a
developer, a specific system/area specialist or an occasional user
providing feedback, please see [CONTRIBUTING.md](CONTRIBUTING.md).

# Installation
It's possible to install the Data Dictionary within a Python environment.

> Prerequisite : A Python interpreter and the Saxon library should be preinstalled

## Procedure
```sh
git clone ssh://git@git.iter.org/imas/data-dictionary.git
cd data_dictionary

pip install . [--user]
```

## Installed Contents
### Directories

The installer creates a directory with the version/tag information prefixed with `dd_` e.g. `dd_3.38.1+40.g8064759`.
It has `include` and `share` directories.

#### The include directory - xml files

XML files including `IDSdef.xml` are copied into the `include` directory. 
$PYTHON_PATH/dd_3.38.1+40.g8064759/include
```
$ ls
core_instant_changes               edge_sources    magnetics           refractometer
core_sources                       edge_transport  mhd_linear          spectrometer_visible
core_transport                     equilibrium     neutron_diagnostic  spectrometer_x_ray_crystal
dd_data_dictionary_validation.txt  IDSDef.xml      pf_active           utilities
dd_data_dictionary.xml             IDSNames.txt    radiation
```
#### The share directory - documentation

Installer installs html documentation. You can find it at following path
```bash
$PYTHON_PATH/share/doc/imas
```
and can be accessible using following commands
```
$ firefox $PYTHON_PATH/share/doc/imas/html_documentation.html
$ dd_doclegacy
```

if you want to generate sphinx documentation on SDCC then you need `Python` and `Saxon`  

For generating IDS Migration guide you need `IMASPy` and `IMAS` should be installed

```bash
pip install -r docs/requirements.txt
python generate_docs.py
pip install .
```

You can access it using following command
```
$ firefox $PYTHON_PATH/share/doc/imas/sphinx/index.html
$ dd_doc
```

### Python scripts

Installer provides `idsinfo` utility which can be used on the command line interface. 

# IDSInfo utility
The `idsinfo` command provides useful features such as showing
metadata, listing all variables, searching for text in IDS fields,
etc.

## Usage

```sh
idsinfo -h
usage: idsinfo [-h] {idspath,metadata,idsnames,search,idsfields,info,doc} ...

IDS Info Utilities

positional arguments:
  {idspath,metadata,idsnames,search,idsfields,info,doc}
                        sub-commands help
    idspath             print ids definition path
    metadata            print metadata
    idsnames            print ids names
    search              Search in ids
    idsfields           shows all fields from ids
    info                Query the IDS XML Definition for documentation
    doc                 Show documentation in the browser

options:
  -h, --help            show this help message and exit

```

## Examples:

### Print data dictionary xml path

```sh
$ idsinfo idspath
/home/ITER/username/.local/dd_3.38.1+15.g41c54bc.dirty/include/IDSDef.xml
```

### Show metadata abot data dictionary

```sh
$ idsinfo metadata
This is Data Dictionary version = 3.38.1-15-g41c54bc, following COCOS = 11
```

### Search in IDS fields

Input: Text to search for
```sh
$ idsinfo search neutron
Searching for 'neutron'.
neutron_diagnostic:
        detectors/green_functions/source_neutron_energies
        detectors/green_functions/source_neutron_energies_error_upper
        .
        .
        synthetic_signals/total_neutron_flux_error_upper
        synthetic_signals/total_neutron_flux_error_lower
        synthetic_signals/total_neutron_flux_error_index
summary:
        fusion/neutron_fluxes
        fusion/neutron_rates
        fusion/neutron_power_total
```

### Print all fields from IDS

Input: IDS name
```sh
$ idsinfo idsfields amns_data
Listing all fields from ids :'amns_data'
ids_properties
ids_properties/comment
ids_properties/homogeneous_time
ids_properties/source
ids_properties/provider
ids_properties/creation_date
ids_properties/version_put
ids_properties/version_put/data_dictionary
ids_properties/version_put/access_layer
ids_properties/version_put/access_layer_language
ids_properties/provenance
ids_properties/provenance/node()
ids_properties/provenance/node()/path
ids_properties/provenance/node()/sources(:)
ids_properties/plugins
.
.
```

### Show information of IDS

```sh
$ idsinfo info amns_data
Atomic, molecular, nuclear and surface physics data. Each occurrence contains the data for a given element (nuclear charge), describing various physical processes. For each process, data tables are organized by charge states. The coordinate system used by the data tables is described under the coordinate_system node.
```

            

Raw data

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    "description": "# IMAS Data Dictionary\n\nThe Data Dictionary is the implementation of the Data Model of ITER's\nIntegrated Modelling & Analysis Suite (IMAS). It describes the\nstructuring and naming of data (as a set of Interface Data Structures\nor IDSs) being used for both simulated and experimental data in a\nmachine agnostic manner.\n\nIDSs are used for standardizing data representation, facilitating\nexploration and comparison, as well as for standardizing coupling\ninterfaces between codes in an Integrated Modelling workflow. The Data\nDictionary itself does not describe explicitly how the data will be\nstored on disk but is used at compile time or at runtime by various\npieces of data access software (e.g. the\n[Access-Layer](https://git.iter.org/projects/IMAS/repos/access-layer)\nwhich handle data archiving and retrieval within applications.\n\nIDSs of the Data Dictionary follow a strict lifecycle that aims at\ncontrolling the compatibility between various releases. This lifecycle\nis fully described in the following external document:\n[ITER_D_QQYMUK](https://user.iter.org/?uid=QQYMUK).\n\nAs it is generic and machine agnostic by design, the IMAS Data Model,\nand by extension its implementation as the Data Dictionary, have the\npotential to serve as a data standard for the fusion community. As\nsuch, it benefits from the wide involvement of specialists and active\nusers and developers in the various areas being described. If you want\nto contribute to the improvement of the Data Dictionary, either as a\ndeveloper, a specific system/area specialist or an occasional user\nproviding feedback, please see [CONTRIBUTING.md](CONTRIBUTING.md).\n\n# Installation\nIt's possible to install the Data Dictionary within a Python environment.\n\n> Prerequisite : A Python interpreter and the Saxon library should be preinstalled\n\n## Procedure\n```sh\ngit clone ssh://git@git.iter.org/imas/data-dictionary.git\ncd data_dictionary\n\npip install . [--user]\n```\n\n## Installed Contents\n### Directories\n\nThe installer creates a directory with the version/tag information prefixed with `dd_` e.g. `dd_3.38.1+40.g8064759`.\nIt has `include` and `share` directories.\n\n#### The include directory - xml files\n\nXML files including `IDSdef.xml` are copied into the `include` directory. \n$PYTHON_PATH/dd_3.38.1+40.g8064759/include\n```\n$ ls\ncore_instant_changes               edge_sources    magnetics           refractometer\ncore_sources                       edge_transport  mhd_linear          spectrometer_visible\ncore_transport                     equilibrium     neutron_diagnostic  spectrometer_x_ray_crystal\ndd_data_dictionary_validation.txt  IDSDef.xml      pf_active           utilities\ndd_data_dictionary.xml             IDSNames.txt    radiation\n```\n#### The share directory - documentation\n\nInstaller installs html documentation. You can find it at following path\n```bash\n$PYTHON_PATH/share/doc/imas\n```\nand can be accessible using following commands\n```\n$ firefox $PYTHON_PATH/share/doc/imas/html_documentation.html\n$ dd_doclegacy\n```\n\nif you want to generate sphinx documentation on SDCC then you need `Python` and `Saxon`  \n\nFor generating IDS Migration guide you need `IMASPy` and `IMAS` should be installed\n\n```bash\npip install -r docs/requirements.txt\npython generate_docs.py\npip install .\n```\n\nYou can access it using following command\n```\n$ firefox $PYTHON_PATH/share/doc/imas/sphinx/index.html\n$ dd_doc\n```\n\n### Python scripts\n\nInstaller provides `idsinfo` utility which can be used on the command line interface. \n\n# IDSInfo utility\nThe `idsinfo` command provides useful features such as showing\nmetadata, listing all variables, searching for text in IDS fields,\netc.\n\n## Usage\n\n```sh\nidsinfo -h\nusage: idsinfo [-h] {idspath,metadata,idsnames,search,idsfields,info,doc} ...\n\nIDS Info Utilities\n\npositional arguments:\n  {idspath,metadata,idsnames,search,idsfields,info,doc}\n                        sub-commands help\n    idspath             print ids definition path\n    metadata            print metadata\n    idsnames            print ids names\n    search              Search in ids\n    idsfields           shows all fields from ids\n    info                Query the IDS XML Definition for documentation\n    doc                 Show documentation in the browser\n\noptions:\n  -h, --help            show this help message and exit\n\n```\n\n## Examples:\n\n### Print data dictionary xml path\n\n```sh\n$ idsinfo idspath\n/home/ITER/username/.local/dd_3.38.1+15.g41c54bc.dirty/include/IDSDef.xml\n```\n\n### Show metadata abot data dictionary\n\n```sh\n$ idsinfo metadata\nThis is Data Dictionary version = 3.38.1-15-g41c54bc, following COCOS = 11\n```\n\n### Search in IDS fields\n\nInput: Text to search for\n```sh\n$ idsinfo search neutron\nSearching for 'neutron'.\nneutron_diagnostic:\n        detectors/green_functions/source_neutron_energies\n        detectors/green_functions/source_neutron_energies_error_upper\n        .\n        .\n        synthetic_signals/total_neutron_flux_error_upper\n        synthetic_signals/total_neutron_flux_error_lower\n        synthetic_signals/total_neutron_flux_error_index\nsummary:\n        fusion/neutron_fluxes\n        fusion/neutron_rates\n        fusion/neutron_power_total\n```\n\n### Print all fields from IDS\n\nInput: IDS name\n```sh\n$ idsinfo idsfields amns_data\nListing all fields from ids :'amns_data'\nids_properties\nids_properties/comment\nids_properties/homogeneous_time\nids_properties/source\nids_properties/provider\nids_properties/creation_date\nids_properties/version_put\nids_properties/version_put/data_dictionary\nids_properties/version_put/access_layer\nids_properties/version_put/access_layer_language\nids_properties/provenance\nids_properties/provenance/node()\nids_properties/provenance/node()/path\nids_properties/provenance/node()/sources(:)\nids_properties/plugins\n.\n.\n```\n\n### Show information of IDS\n\n```sh\n$ idsinfo info amns_data\nAtomic, molecular, nuclear and surface physics data. Each occurrence contains the data for a given element (nuclear charge), describing various physical processes. For each process, data tables are organized by charge states. The coordinate system used by the data tables is described under the coordinate_system node.\n```\n",
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