Web Service Phylogenetics_AT_JST REST It

aka Phylogenetics_AT_JST Add_annotation_inactiveAdd_annotation_inactiveLog in to add alternative_name
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Annotations: 22 Total number of annotations from the provider's definition / description document. 0 Total number of annotations submitted by members of BiodiversityCatalogue. 22 Total number of annotations sourced from other registries. 0

Overview

Provider:
Icon  INFN Bari

Location:
Italy It

Submitter/Source:
Pasquale NotarangeloIt (over 5 years ago)

Base URL:
http://alicegrid17.ba.infn.it:8080/INFN.Grid.RestFrontEnd/QueryJob

Description(s):
by Saverio Vicario (about 5 years ago)

The web service JST offer a large set of method to define model, perform, test and use phylogenetic inference in downstream application. details are in the endpoints

by Saverio Vicario (almost 5 years ago)

It should be noted that JST offer asynchronous interaction. It means that all the endpoints with bioinformatic names (and tag “method”) are tools to submit a job and their answer is simply a reference to be used to retrived a single job or several jobs using the two retrival job services

by Saverio Vicario (over 4 years ago)

Documentation for the use of the service

All the asynchronous services (services which have long run runtime) that were developed ex-novo within BioVeL have the same interface.

For each service provider ( i.e. INFN) 3 types of endpoint exists:

  1. job submission,
  2. job retrieval,
  3. multiple jobs retrieval.

Job submission

The job submission endpoint has four parameters:

  1. name — required
  2. arguments — required
  3. sessionid — optional
  4. email — optional

name differentiates the different types of work. A different entry in Biodiversity catalogue exist for each possible value of name. Within this entry the details of the formatting for the body of arguments are given.

arguments give the information. Data are given as URL(s) . Multiple submission are divided by “;” within the body of arguments.

Job retrieval

The endpoint to collect results of a single job has one parameter, jobid, obtained in the reply of the submission. The reply is for example:

<Jobs>
    <Job>
    <Arguments> http://webtest.ba.infn.it/vicario/FinalFusariumDB_2.nex 5700.fa 10589.fbsse se selknlk noiho niooih r </Arguments>
    <Comment>interactive</Comment> 
    <CPUs>7</CPUs>
    <Flag>2dbbd030-2803-43c0-a21d-369a21e17f2b</Flag>
    <Id>349177</Id> 
    <LastCheck>2011-11-18 12:54:01.0</LastCheck>
   <Name>MyBlasts</Name> 
   <Output/> <Provenance/>
   <Status>free</Status>
   </Job>
</Jobs>

Multiple jobs retrieval

The endpoint to collect results of several jobs submitted in the same argument body use the Flag value obtained as reply to submission. The reply is identical to previous service only that several tag Job exist

The cited taverna components are looking for these paths within the reply:

  1. /Jobs/Job/Status to check if is equal to done.
  2. /Jobs/Job/Output to collect the body that could be or an xml or url or a base64 encoded string. Generally is a URL with bulk information not relevant for the taverna engine but to pass on to next webservice.
  3. /Jobs/Job/StandardOutput to collect the body that could be or an xml or url or a base64 encoded string. Generally is a XML with information to be processed within the taverna engine
  4. /Jobs/Job/StandardError to collect the body that is a base64 encoded string with all relevant info for debug error

Use of the service within a Taverna workflow engine

The service presented are embedded within workflow and component. Components are workflow ready to be reused in other workflow. Two components ( JSTAsync1, JSTAsync2) with the different endpoints of this service, depending if the endpoint use base64 encoding the standardoutput. The taverna schema of the two components is here shown. The top blue box is the call to the submit job endpoint, while the second blue box within the nested workflow is the repeated request of retrieval to the single job retrieval endpoint. The four yellow box use XPath to extract the 4 already cited path from the XML of reply.

MediumMedium

This two generic component workflow are then used in a series of specialized component workflow that format correctly the argument body and parse the outputs for downstream applications.

Here the table of all services linked to biodiversity catalogue, with link to specialized component and the meaning of the body of the tag StandardOuput and Output. The tag StandardError gives always the last 200 lines of the standardouput + standarderror stream of the unix process, always base64 encoded.

NameWikiComponent WFOuputStandardOuputbase64 encoded?
consensus_xmlLinkLinkURL of targz folderXML with tag tree for each newickFalse
MrBayesPPtestLinkLinkURL of targz folderXML with description attributesFalse
itolLinkLinkURL of targz folderurl to see tree in ITOL websiteTrue
MrBayes_16CPUsLinkLinkURL of targz folderlist file of previous URLFalse
PartitionFinderLinkLinkURL of targz folderbest model description in textTrue
geoks_xmlLinkLinkURL of targz folderXML with description attributesfalse
phyloHwikiLinkURL of targz folderHtml output
by Saverio Vicario (over 4 years ago)

The Phylogenetic_at_JST WS is the result of the cooperation between CNR (Italian Research National Council) and INFN (National Institute of Nuclear Physics) within the Project BioVeL.

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ELIXIR Description(s): Info
No info yet
Cost: Info
No info yet
Usage conditions: Info
by Saverio Vicario (almost 5 years ago)

max 1 request per second

Contact info: Info
by Jon Giddy Admin(almost 5 years ago)

Pasquale Notarangelo, INFN (pasquale.notarangelo@ba.infn.it)

Citations of this service: Info
by Saverio Vicario (almost 5 years ago)

@article{Vicario2012, author = {Vicario, Saverio and Balech, Bachir and Donvito, Giacinto and Notarangelo, Pasquale and Pesole, Graziano}, doi = {10.14806/ej.18.B.557}, file = , issn = {2226-6089}, journal = {EMBnet.journal}, month = nov, number = {B}, pages = {77}, title = {{The BioVel Project: Robust phylogenetic workflows running on the GRID}}, url = {http://journal.embnet.org/index.php/embnetjournal/article/view/557}, volume = {18}, year = {2012} }

Maturity level of this service (from the BioVeL wiki) and actions to improve it: Info
by Aleksandra Nenadic Admin(over 4 years ago)
https://wiki.biovel.eu/display/doc/BioVeL+Service+-+Phylogenetics_AT_JST

Actions to improve the service description

Provisional maturity level: 3 (subject to manual review)

Highest maturity level - no further actions required.

Info Members Responsible for this Service (3)

Info Favourited By (1)