# `votable` or `VOTLibRust` Library to build, edit, read and write [VOTables](https://www.ivoa.net/documents/VOTable/) in Rust and to convert them efficiently back and forth in standard XML-TABLEDATA, XML-BINARY, XML-BINARY2 and non-standard JSON, YAML and TOML while preserving all elements (except comments) and their order. [![](https://img.shields.io/crates/v/votable.svg)](https://crates.io/crates/votable) [![](https://img.shields.io/crates/d/votable.svg)](https://crates.io/crates/votable) [![API Documentation on docs.rs](https://docs.rs/votable/badge.svg)](https://docs.rs/votable/) [![BenchLib](https://github.com/cds-astro/cds-votable-rust/actions/workflows/libtest.yml/badge.svg)](https://github.com/cds-astro/cds-moc-rust/actions/workflows/libtest.yml) VOT Lib Rust is used in: * [VOTCli](https://github.com/cds-astro/cds-votable-rust/tree/main/crates/cli) edit and convert VOTables from the command line; * [VOTWasm](https://github.com/cds-astro/cds-votable-rust/tree/main/crates/wasm) read/write and convert VOTables in Web Browsers. * [Aladin Lite V3](https://github.com/cds-astro/aladin-lite) ## Status The code contains all main functionalities: * supports BINARY, BINARY2 formats * supports CDATA in rows, StAX mode for streaming * supports MIVOT block parsing But is not yet 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](https://github.com/cds-astro/aladin-lite/tree/develop) * 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](https://serde.rs/). 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](https://www.ivoa.net/documents/VOTable/20191021/REC-VOTable-1.4-20191021.html)) 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 *LINK*s, 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. * We do not support VOTable such as (example provided by Mark Taylor): ```xml 4'> ]> &td3;
0
1
2
 ``` since [quick_xml](https://github.com/tafia/quick-xml) so far does not cope with declared entities, see [this issue](https://github.com/tafia/quick-xml/issues/258). ## Other way to convert from VOTable to JSON The XML2JSON conversion has been exercised by [Laurent Michel](https://github.com/lmichel) in the context of the processing of model annotations in VOTables ([the MIVOT](https://github.com/ivoa-std/ModelInstanceInVot)). The use case is to convert model instances, serialized in XML, into JSON messages. The conversion is using standard Python tools ([xmltodic](https://pypi.org/project/xmltodict/) module). The code below is extracted from the [client code](https://github.com/ivoa/modelinstanceinvot-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](https://github.com/bramstein/xsltjson). ```python 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) ```rust 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 VizieR Astronomical Server vizier.u-strasbg.fr Photometric and spectroscopic catalog of objects in the field around HE0226-4110 SDSS photometric catalog Right Ascension of the object (ICRS) (ra) [*] Multiple SDSS12 name [4/38]? Model magnitude in u filter, AB scale (u) (5)
NaN * 14.52
1.25 -1.2
truncated result (maxtup=2) ``` ### JSON ```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 ```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=${SDSS12}' [[votable.resources.sub_elems.resource_or_table.elems]] elem_type = 'Field' name = 'umag' datatype = 'float' unit = 'mag' precision = '3' width = 2 ucd = 'phot.mag;em.opt.U' description = '[4/38]? Model magnitude in u filter, AB scale (u) (5)' [votable.resources.sub_elems.resource_or_table.elems.values] null = 'NaN' [votable.resources.sub_elems.resource_or_table.data] data_type = 'TableData' rows = [ [ nan, '*', 14.52, ], [ 1.25, '', -1.2, ], ] [[votable.resources.sub_elems.infos]] name = 'QUERY_STATUS' value = 'OVERFLOW' content = 'truncated result (maxtup=2)' ``` ### YAML ```yaml votable: ID: my_votable version: '1.4' description: VizieR Astronomical Server vizier.u-strasbg.fr elems: - elem_type: Info ID: VERSION name: votable-version value: 1.99+ (14-Oct-2013) resources: - ID: yCat_17011219 name: J/ApJ/701/1219 description: Photometric and spectroscopic catalog of objects in the field around HE0226-4110 elems: - elem_type: CooSys ID: J2000 system: eq_FK4 equinox: 2000.0 - elem_type: CooSys ID: J2015.5 system: ICRS epoch: 2015.5 sub_elems: - resource_or_table: elem_type: Table id: V_147_sdss12 name: V/147/sdss12 description: SDSS photometric catalog elems: - elem_type: Field name: RA_ICRS datatype: double unit: deg precision: '6' width: 10 ucd: pos.eq.ra;meta.main description: Right Ascension of the object (ICRS) (ra) - elem_type: Field name: m_SDSS12 datatype: char precision: '6' width: 10 ucd: meta.code.multip arraysize: '1' description: '[*] Multiple SDSS12 name' links: - href: http://vizier.u-strasbg.fr/viz-bin/VizieR-4?-info=XML&-out.add=.&-source=V/147&SDSS12=${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 ```rust 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 * [X] Support `CDATA` + [X] Support in `Info`, `Description`, `Link`, `PARAMRef` and `FIELDRef` + [X] Support `CDATA` in `` * [ ] 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...) * [X] 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! * [X] Add possibility to convert to/from `TABLEDATA`, `BINARY`, `BINARY2` + but still to implement streaming mode in CLI * [X] 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 * Apache License, Version 2.0, ([LICENSE-APACHE](LICENSE-APACHE) or http://www.apache.org/licenses/LICENSE-2.0) * MIT license ([LICENSE-MIT](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.