`votable` or `VOTLibRust`

Library to read/write VOTables in Rust and to convert them in JSON, YAML, TOML and back to XML.

VOT Lib Rust is used in:

VOTCli convert VOTables from the command line;
VOTWasm read/write and convert VOTables in Web Browsers.

Status

This library is in an early stage of development.
We are (reasonably) open to changes in the various format, e.g.:

we could flag attributes with a '@' prefix
we could use upper case elements tag names
we could remove the 's' suffix in elements arrays
we could change the post_infos name for something else
...

More testing is required, especially the bit type and arrays. Please, provide us with your VOTable examples!

Why JSON, TOML, YAML in addition to XML

VOTable is an XML based format. Why other formats?

JSON: to easily manipulate VOTable data in Web Browsers since JSON represent JavaScript objects (and all browsers parse JSON into JavaScript objects natively).
TOML: to easily update manually VOTables (especially the metadata part of VOTables). Moreover, it is quite compact.
YAML: because some people like it, and it was almost free to implement (thanks to serde).

Motivations

Support natively the VOTable format in the new CDS internal tool qat2s (tool to query and manipulate possibly large catalogues with multi-thread capabilities).
Store VizieR (large) catalogues rich metadata in a user friendly format (TOML) while being able to return the same VOTable header as VizieR (without using a database connexion).
- for qat2s, ExXmatch, progressive catalogue
Add a Rust VOTable parsing and writting library for Aladin Lite V3
...

Design choices and problems

The default provided implementation converting from JSON/YAML/TOML does not focus on performancs since we do not use the VOTable FIELDs information but deserialize each table field in the first succeeding VOTableValue (see votable::impls::Schema.serialize_seed).

VOT Lib resort heavily on serde.

This library has been design to preserve the order of VOTable TAGs when converting back on forth in XML, JSON, ...
But, so far:

XML comments are ignored and lost ;
CDATA block are ignored and lost.

In JSON/TOML/YAML, for the VOTABLE and RESOURCE elements, we make a difference between INFO blocks located before and after the RESOURCE element(s). We use infos (only for RESOURCE) and post_infos arrays. Quoting the IVOA document:

The INFO element may occur before the closing tags /TABLE and /RESOURCE and /VOTABLE (enables post-operational diagnostics)

(we wonder if post-operational diagnostics should not have a name different from INFO in VOTables).

In JSON/TOML/YAML, for VOTABLE, RESOURCE, TABLE and GROUP elements, we group together the "open bullet" (see 7.1 of the VOTable standard) elements in an elements array containing objects having an "elem_type" attribute set to one of: Info, Field, Coosys, Timesys, Group, Param, ...

Internally we make a difference (different struct/class) between GROUP in VOTABLE and RESOURCE from GROUP in TABLE since in the later case the GROUP may contain FIELDRef.

In JSON/TOML/YAML, there is no difference between attribute and sub-elements names (all in camel case).

WARNINGS

TOML does not supports null (we so far convert null values by an empty string).
The default provided implementation loads all data in memory, so it is not adapted for large files!

Other way to convert from VOTable to JSON

The XML2JSON conversion has been exercised by Laurent Michel in the context of the processing of model annotations in VOTables (the MIVOT). The use case is to convert model instances, serialized in XML, into JSON messages.
The conversion is using standard Python tools (xmltodic module). The code below is extracted from the client code project. It is to be noted that the translation rules are not PYTHON (nor VOTable) specific, they are also implemented in e.g. XSLT.

import os
import xmltodict
import json
import numpy
from lxml import etree

class MyEncoder(json.JSONEncoder):

  def default(self, obj):
    if isinstance(obj, numpy.integer):
      return int(obj)
    elif isinstance(obj, numpy.floating):
      return float(obj)
    elif isinstance(obj, numpy.ndarray):
      return obj.tolist()
    else:
      return super(MyEncoder, self).default(obj)

data_path = os.path.dirname(os.path.realpath(__file__))

xml_block = etree.parse(os.path.join(data_path, "votable_to_json.xml"))
raw_json = xmltodict.parse(etree.tostring(xml_block))
pretty_json = json.dumps(raw_json, indent=2, cls=MyEncoder)
print(pretty_json)

with open(os.path.join(data_path, "votable_to_json.json"), 'w') as file:
  file.write(json.dumps(raw_json, indent=2))

Advantages:

standard
few lines of python

Inconvenient:

the order of elements (especially INFOs and post processing INFOs) is lost
it is a one way conversion (not possible to then convert from JSON to VOTable)

Example

Several outputs obtained from the same API made VOTable.

Rust code (API created VOTable)

let rows = vec![
    vec![VOTableValue::Double(f64::NAN), VOTableValue::CharASCII('*'), VOTableValue::Float(14.52)],
    vec![VOTableValue::Double(1.25), VOTableValue::Null, VOTableValue::Float(-1.2)],
];

let data_content = InMemTableDataRows::new(rows);

let table = Table::new()
  .set_id("V_147_sdss12")
  .set_name("V/147/sdss12")
  .set_description("SDSS photometric catalog".into())
  .push_field(
    Field::new("RA_ICRS", Datatype::Double)
      .set_unit("deg")
      .set_ucd("pos.eq.ra;meta.main")
      .set_width(10)
      .set_precision(Precision::new_dec(6))
      .set_description("Right Ascension of the object (ICRS) (ra)".into())
  ).push_field(
    Field::new("m_SDSS12", Datatype::CharASCII)
      .set_ucd("meta.code.multip")
      .set_arraysize("1")
      .set_width(10)
      .set_precision(Precision::new_dec(6))
      .set_description("[*] Multiple SDSS12 name".into())
      .push_link(Link::new().set_href("http://vizier.u-strasbg.fr/viz-bin/VizieR-4?-info=XML&-out.add=.&-source=V/147&SDSS12=${SDSS12}"))
  ).push_field(
    Field::new("umag", Datatype::Float)
      .set_unit("mag")
      .set_ucd("phot.mag;em.opt.U")
      .set_width(6)
      .set_precision(Precision::new_dec(3))
      .set_description("[4/38]? Model magnitude in u filter, AB scale (u) (5)".into())
      .set_values(Values::new().set_null("NaN"))
  ).set_data(Data::new_empty().set_tabledata(data_content));

let resource = Resource::default()
  .set_id("yCat_17011219")
  .set_name("J/ApJ/701/1219")
  .set_description(r#"Photometric and spectroscopic catalog of objects in the field around HE0226-4110"#.into())
  .push_coosys(CooSys::new("J2000", System::new_default_eq_fk5()))
  .push_coosys(CooSys::new("J2015.5", System::new_icrs().set_epoch(2015.5)))
  .push_table(table)
  .push_post_info(Info::new("QUERY_STATUS", "OVERFLOW").set_content("truncated result (maxtup=2)"));

let mut votable = VOTable::new(resource)
  .set_id("my_votable")
  .set_version(Version::V1_4)
  .set_description(r#"VizieR Astronomical Server vizier.u-strasbg.fr"#.into())
  .push_info(Info::new("votable-version", "1.99+ (14-Oct-2013)").set_id("VERSION"));

Remark: the coherence between user input VOTableValue and declared Fields is checked only when serializing in BINARY or BINARY2.

VOTable

<?xml version="1.0" encoding="UTF-8"?>
<VOTABLE ID="my_votable" version="1.4">
    <DESCRIPTION>VizieR Astronomical Server vizier.u-strasbg.fr</DESCRIPTION>
    <INFO ID="VERSION" name="votable-version" value="1.99+ (14-Oct-2013)"/>
    <RESOURCE ID="yCat_17011219" name="J/ApJ/701/1219">
        <DESCRIPTION>Photometric and spectroscopic catalog of objects in the field around HE0226-4110</DESCRIPTION>
        <COOSYS ID="J2000" system="eq_FK4" equinox="B2000"/>
        <COOSYS ID="J2015.5" system="ICRS" epoch="J2015.5"/>
        <TABLE ID="V_147_sdss12" name="V/147/sdss12">
            <DESCRIPTION>SDSS photometric catalog</DESCRIPTION>
            <FIELD name="RA_ICRS" datatype="double" unit="deg" precision="6" width="10" ucd="pos.eq.ra;meta.main">
                <DESCRIPTION>Right Ascension of the object (ICRS) (ra)</DESCRIPTION>
            </FIELD>
            <FIELD name="m_SDSS12" datatype="char" precision="6" width="10" ucd="meta.code.multip" arraysize="1">
                <DESCRIPTION>[*] Multiple SDSS12 name</DESCRIPTION>
                <LINK href="http://vizier.u-strasbg.fr/viz-bin/VizieR-4?-info=XML&amp;-out.add=.&amp;-source=V/147&amp;SDSS12=${SDSS12}"/>
            </FIELD>
            <FIELD name="umag" datatype="float" unit="mag" precision="3" width="6" ucd="phot.mag;em.opt.U">
                <DESCRIPTION>[4/38]? Model magnitude in u filter, AB scale (u) (5)</DESCRIPTION>
                <VALUES null="NaN"/>
            </FIELD>
            <DATA>
                <TABLEDATA>
                    <TR>
                        <TD>NaN</TD>
                        <TD>*</TD>
                        <TD>14.52</TD>
                    </TR>
                    <TR>
                        <TD>1.25</TD>
                        <TD></TD>
                        <TD>-1.2</TD>
                    </TR>
                </TABLEDATA>
            </DATA>
        </TABLE>
        <INFO name="QUERY_STATUS" value="OVERFLOW">truncated result (maxtup=2)</INFO>
    </RESOURCE>
</VOTABLE>

JSON

{
  "votable": {
    "ID": "my_votable",
    "version": "1.4",
    "description": "VizieR Astronomical Server vizier.u-strasbg.fr",
    "elems": [
      {
        "elem_type": "Info",
        "ID": "VERSION",
        "name": "votable-version",
        "value": "1.99+ (14-Oct-2013)"
      }
    ],
    "resources": [
      {
        "ID": "yCat_17011219",
        "name": "J/ApJ/701/1219",
        "description": "Photometric and spectroscopic catalog of objects in the field around HE0226-4110",
        "elems": [
          {
            "elem_type": "CooSys",
            "ID": "J2000",
            "system": "eq_FK4",
            "equinox": 2000.0
          },
          {
            "elem_type": "CooSys",
            "ID": "J2015.5",
            "system": "ICRS",
            "epoch": 2015.5
          }
        ],
        "tables": [
          {
            "id": "V_147_sdss12",
            "name": "V/147/sdss12",
            "description": "SDSS photometric catalog",
            "elems": [
              {
                "elem_type": "Field",
                "name": "RA_ICRS",
                "datatype": "double",
                "unit": "deg",
                "precision": "6",
                "width": 10,
                "ucd": "pos.eq.ra;meta.main",
                "description": "Right Ascension of the object (ICRS) (ra)"
              },
              {
                "elem_type": "Field",
                "name": "m_SDSS12",
                "datatype": "char",
                "precision": "6",
                "width": 10,
                "ucd": "meta.code.multip",
                "arraysize": "1",
                "description": "[*] Multiple SDSS12 name",
                "links": [
                  {
                    "href": "http://vizier.u-strasbg.fr/viz-bin/VizieR-4?-info=XML&-out.add=.&-source=V/147&SDSS12=${SDSS12}"
                  }
                ]
              },
              {
                "elem_type": "Field",
                "name": "umag",
                "datatype": "float",
                "unit": "mag",
                "precision": "3",
                "width": 6,
                "ucd": "phot.mag;em.opt.U",
                "description": "[4/38]? Model magnitude in u filter, AB scale (u) (5)",
                "values": {
                  "null": "NaN"
                }
              }
            ],
            "data": {
              "data_type": "TableData",
              "rows": [
                [
                  null,
                  "*",
                  14.52
                ],
                [
                  1.25,
                  null,
                  -1.2
                ]
              ]
            }
          }
        ],
        "post_infos": [
          {
            "name": "QUERY_STATUS",
            "value": "OVERFLOW",
            "content": "truncated result (maxtup=2)"
          }
        ]
      }
    ]
  }
}

TOML

[votable]
ID = 'my_votable'
version = '1.4'
description = 'VizieR Astronomical Server vizier.u-strasbg.fr'

[[votable.elems]]
elem_type = 'Info'
ID = 'VERSION'
name = 'votable-version'
value = '1.99+ (14-Oct-2013)'

[[votable.resources]]
ID = 'yCat_17011219'
name = 'J/ApJ/701/1219'
description = 'Photometric and spectroscopic catalog of objects in the field around HE0226-4110'

[[votable.resources.elems]]
elem_type = 'CooSys'
ID = 'J2000'
system = 'eq_FK4'
equinox = 2000.0

[[votable.resources.elems]]
elem_type = 'CooSys'
ID = 'J2015.5'
system = 'ICRS'
epoch = 2015.5

[[votable.resources.tables]]
id = 'V_147_sdss12'
name = 'V/147/sdss12'
description = 'SDSS photometric catalog'

[[votable.resources.tables.elems]]
elem_type = 'Field'
name = 'RA_ICRS'
datatype = 'double'
unit = 'deg'
precision = '6'
width = 10
ucd = 'pos.eq.ra;meta.main'
description = 'Right Ascension of the object (ICRS) (ra)'

[[votable.resources.tables.elems]]
elem_type = 'Field'
name = 'm_SDSS12'
datatype = 'char'
precision = '6'
width = 10
ucd = 'meta.code.multip'
arraysize = '1'
description = '[*] Multiple SDSS12 name'

[[votable.resources.tables.elems.links]]
href = 'http://vizier.u-strasbg.fr/viz-bin/VizieR-4?-info=XML&-out.add=.&-source=V/147&SDSS12=${SDSS12}'

[[votable.resources.tables.elems]]
elem_type = 'Field'
name = 'umag'
datatype = 'float'
unit = 'mag'
precision = '3'
width = 6
ucd = 'phot.mag;em.opt.U'
description = '[4/38]? Model magnitude in u filter, AB scale (u) (5)'

[votable.resources.tables.elems.values]
null = 'NaN'

[votable.resources.tables.data]
data_type = 'TableData'
rows = [
    [
    nan,
    '*',
    14.52,
],
    [
    1.25,
    '',
    -1.2,
],
]

[[votable.resources.post_infos]]
name = 'QUERY_STATUS'
value = 'OVERFLOW'
content = 'truncated result (maxtup=2)'

YAML

votable:
  ID: my_votable
  version: '1.4'
  description: VizieR Astronomical Server vizier.u-strasbg.fr
  elems:
  - elem_type: Info
    ID: VERSION
    name: votable-version
    value: 1.99+ (14-Oct-2013)
  resources:
  - ID: yCat_17011219
    name: J/ApJ/701/1219
    description: Photometric and spectroscopic catalog of objects in the field around
      HE0226-4110
    elems:
    - elem_type: CooSys
      ID: J2000
      system: eq_FK4
      equinox: 2000.0
    - elem_type: CooSys
      ID: J2015.5
      system: ICRS
      epoch: 2015.5
    tables:
    - id: V_147_sdss12
      name: V/147/sdss12
      description: SDSS photometric catalog
      elems:
      - elem_type: Field
        name: RA_ICRS
        datatype: double
        unit: deg
        precision: '6'
        width: 10
        ucd: pos.eq.ra;meta.main
        description: Right Ascension of the object (ICRS) (ra)
      - elem_type: Field
        name: m_SDSS12
        datatype: char
        precision: '6'
        width: 10
        ucd: meta.code.multip
        arraysize: '1'
        description: '[*] Multiple SDSS12 name'
        links:
        - href: http://vizier.u-strasbg.fr/viz-bin/VizieR-4?-info=XML&-out.add=.&-source=V/147&SDSS12=${SDSS12}
      - elem_type: Field
        name: umag
        datatype: float
        unit: mag
        precision: '3'
        width: 6
        ucd: phot.mag;em.opt.U
        description: '[4/38]? Model magnitude in u filter, AB scale (u) (5)'
        values:
          'null': NaN
      data:
        data_type: TableData
        rows:
        - - .nan
          - '*'
          - 14.52
        - - 1.25
          - null
          - -1.2
    post_infos:
    - name: QUERY_STATUS
      value: OVERFLOW
      content: truncated result (maxtup=2)

Example: Iterate on both Tables and Rows of a VOTable

    let mut votable_it = VOTableIterator::from_file("resources/sdss12.vot")?;
    while let Some(mut row_it) = votable_it.next_table_row_value_iter()? {
      let table_ref_mut = row_it.table();
      println!("Fields: {:?}", table_ref_mut.elems);
      for (i, row) in row_it.enumerate() {
        println!("Row {}: {:?}", i, row);
      }
    }
    let votable = votable_it.end_of_it();
    println!("VOTable: {:?}", votable);

To-do list

Support CDATA?
Fill the doc for the Rust library (but I so far do not know people interested in such a lib since Rust is not very used in the astronomy community so far, so...)
Add a check method ensuring that user input VOTAbleValue (using the API to build a VOTable) matches the table schema (or automatically converting in the right VOTableValue)
Add much more tests!
Add possibility to convert to/from TABLEDATA, BINARY, BINARY2
Enrich votable::impls::Schema.serialize_seed (possible bugs when deserializing JSON/TOML/YAML arrays and converting to BINARY or BINARY2)
Write a custom deserializer for VOTableValue (look at cargo-expand output for a basis)
Implements toCSV (but not fromCSV)
...

License

Like most projects in Rust, this project is licensed under either of

Apache License, Version 2.0, (LICENSE-APACHE or http://www.apache.org/licenses/LICENSE-2.0)
MIT license (LICENSE-MIT or http://opensource.org/licenses/MIT)

at your option.

Contribution

Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in this project by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any additional terms or conditions.

votable 0.2.1

votable or VOTLibRust