biovel-nbc
Naturalis implementations of BioVeL services.
Contributors
- Bachir Balech (bitbucket: bachirb)
- Rutger Vos, @rvosa
- Christian Brenninkmeijer, @Christian-B
- Hannes Hettling, @hettling
- David King, @DauvitKing
Aims
- To develop command-line tools that merge data in a number of commonly-used phylogenetic file formats and export them as NeXML: the Merger service.
- To develop command-line tools that extract objects from NeXML data: Taxa, Trees, Character matrices, all with metadata embedded: the Extractor service.
- To wrap these tools inside Taverna-compatible RESTful services.
- To publish these services on BiodiversityCatalogue.
- To annotate these services according to BioVeL guidelines.
The Merger service
Inputs
- Phylogenetic trees, in at least the following formats: Newick, NEXUS, PhyloXML, NeXML.
There are two parameters for specifying trees, the location (
trees={URL}),
and the syntax format (treeformat={Newick|NEXUS|PhyloXML|NeXML}). - Alignments, in at least the following formats: PHYLIP, NEXUS, NeXML, FASTA. There are
three parameters for each alignment file, the location (
data={URL}), the syntax format (dataformat={PHYLIP|NEXUS|NeXML|FASTA}), and, optionally, the data type (datatype={dna|protein|standard}, default is dna). - Character sets, in text format, i.e.
charsets={URL},charsetformat={nexus|txt}. - Metadata in JSON or TSV syntax. i.e.
meta={URL},metaformat={JSON|TSV}. The first column of the metadata identifies which object is annotated. We can distinguish the following objects:TaxonID, AlignmentID, TreeID, NodeID, SiteID, CharacterID
Output
- A NeXML document.
URL API
- The service responds to HTTP GET requests, so all parameters are combined in the QUERY_STRING, with all "dangerous" characters URL-escaped.
The Extractor service
Inputs
- NeXML file, whose location is specified as a URL, e.g.
nexml={URL} - A parameter that specifies which objects to extract, e.g.
objects={Taxa|Trees|Matrices|Charsets} - A parameter that specifies the output formats,
treeformat={NEXUS|Newick|PhyloXML|NeXML},dataformat={NEXUS|PHYLIP|FASTA|Stockholm},metaformat={tsv|JSON|csv},charsetformat={NEXUS|JSON}
Output
- A subset of the NeXML data in the requested format, with a separate download of the metadata, likewise in the requested format.
Service deployment
We deploy the services as mod_perl handlers, which means that for synchronous services (i.e. everything is done in one request/response cycle) no forking is done at all. For asynchronous servers, the service class doesn't have to keep track of its session: the superclass keeps track of serializing and de-serializing the job object between requests.
To deploy the services, there is a puppet manifest that installs the dependencies and configures apache on a Vagrant box here: vm/manifests/default.pp, and for rackspace-hosted, default Ubuntu flavours here: vm/manifests/rackspace.pp
Links
Build status
Currently, the build status is:
