votable

Crates.iovotable
lib.rsvotable
version0.6.0
sourcesrc
created_at2022-10-06 13:32:24.66519
updated_at2024-04-05 15:17:59.458584
descriptionRust implementation of a VOTable serializer/deserializer with support for format other than XML, such as JSON, TOML or YAML.
homepagehttps://github.com/cds-astro/cds-votable-rust/
repositoryhttps://github.com/cds-astro/cds-votable-rust/
max_upload_size
id681339
size745,494
Fran├žois-Xavier Pineau (fxpineau)

documentation

https://docs.rs/votable

README

votable or VOTLibRust

Library to build, read and write VOTables in Rust and to convert them efficiently back and forth in JSON, YAML, TOML, XML-TABLEDATA, XML-BINARY and XML-BINARY2 while preserving all elements (except comments) and their order.

API Documentation on docs.rs BenchLib

VOT Lib Rust is used in:

Status

The code contains all main functionalities:

  • supports BINARY, BINARY2 formats
  • supports CDATA in rows, StAX mode for streaming
  • supports MIVOT block parsing

But it is far from been as clean and documented as I would like. If you want to use this crate in a Rust project, you should probably have a look at the VOTCli code.

We are still (reasonably) open to changes, 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 writing library for Aladin Lite V3
  • Ensure statically the in-memory built structure is compliant with a VOTable
  • ...

Design choices and problems

Although the default provided implementation converting from JSON/YAML/TOML does not focus on performances 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), performances seems to be good nevertheless.

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.

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 a RESOURCE, we pack together LINKs, a sub-RESOURCE or a TABLE and INFO together in a ResourceSubElem structure.

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

WARNINGS

  • TOML does not support null (we so far convert null values by an empty string).
  • Conversions from/to TOML/JSON/YAML requires all data to be loaded in memory, 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(ArraySize::new_fixed_1d(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_sub_elem(
    ResourceSubElem::from_table(table)
      .push_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="2" 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
          }
        ],
        "sub_elems": [
          {
            "resource_or_table": {
              "elem_type": "Table",
              "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": 2,
                  "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
                  ]
                ]
              }
            },
            "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.sub_elems]]
[votable.resources.sub_elems.resource_or_table]
elem_type = 'Table'
id = 'V_147_sdss12'
name = 'V/147/sdss12'
description = 'SDSS photometric catalog'

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

[[votable.resources.sub_elems.resource_or_table.elems]]
elem_type = 'Field'
name = 'umag'
datatype = 'float'
unit = 'mag'
precision = '3'
width = 2
ucd = 'phot.mag;em.opt.U'
description = '[4/38]? Model magnitude in u filter, AB scale (u) (5)'

[votable.resources.sub_elems.resource_or_table.elems.values]
null = 'NaN'

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

[[votable.resources.sub_elems.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
      sub_elems:
        - resource_or_table:
            elem_type: Table
            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: 2
                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
          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

    • Support in Info, Description, Link, PARAMRef and FIELDRef
    • Support CDATA in <TD></TD>
  • 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

    • but still to implement streaming mode in CLI
  • Implements toCSV (but not fromCSV) in CLI

  • Replace quick_error by anyhow and thiserror.

  • Bump quick_xml version and:

    • Implement parsing without copy from &[u8] (when full data in men, e.g. in wasm, or for memmapped files)
    • Implement async
  • ...

License

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

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.

Commit count: 180

cargo fmt