Module: SLiMParser Description: SLiMSuite REST output parsing tool. Version: 0.6.0 Last Edit: 22/05/19 Citation: Edwards et al. (2020), Methods Mol Biol. 2141:37-72.

Copyright © 2014 Richard J. Edwards - See source code for GNU License Notice

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Imported modules: rje rje_obj rje_html

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See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This module is for parsing the full REST output of a program into a couple of dictionaries, with options to output the data to files or convert to/from json format.

If restin=FILE is a URL, this will be interpreted as a REST command for API access. Use with rest=X and pureapi=T to print the output to STDOUT once the run is complete. Use in conjunction with v=-1 to avoid additional STDOUT output and silent=T to avoid log generation.

REST URLs can include files to be uploaded. These must be prefixed with file:, e.g. &seqin=file:input.fas. If the specified file exists then the content will replace the file name in the REST call.

Commandline

INPUT/OUTPUT OPTIONS

restin=FILE # Full REST output file, REST jobid (number), or full REST call URL (http://...) []
password=X # Optional password for REST jobid retrieval [None]
restout=T/F # Whether to save extracted elements to individual files [False]
rest=X # Return text for just the REST output element X []
restbase=X # Basefile for parsed REST output that lacks defined filename [jobid]
restoutdir=PATH # Path for output of parsed REST output [./]
pureapi=T/F # Whether to return the text returned from the REST call. Needs rest=X. [False]

REST API Options

resturl=X # URL of rest server ['http://rest.slimsuite.unsw.edu.au/']
refresh=X # Initial number of seconds for between checks for job status (will double) [5]
maxrefresh=X # Maximum number of seconds for incrementing check refresh [600]

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See also rje.py generic commandline options.

History Module Version History

    # 0.0.0 - Initial Compilation.
    # 0.0.1 - Fixed RestKeys bug.
    # 0.1.0 - Added retrieval and parsing of existing server job. Added password.
    # 0.2.0 - Added API access to REST server if restin is REST call (i.e. starts with http:)
    # 0.2.1 - Added PureAPI output of API REST call returned text.
    # 0.3.0 - Added parsing of input files to give to rest calls.
    # 0.3.1 - Fixed issue that had broken REST server full output.
    # 0.3.2 - Fixed issue reading files for full output.
    # 0.3.3 - Tidied output names when restbase=jobid.
    # 0.3.4 - Tweaked error messages.
    # 0.4.0 - Added simple json format output.
    # 0.5.0 - Added restkeys/outputs output of REST output keys.
    # 0.5.1 - Minor docs and bug fixes.
    # 0.6.0 - Improved functionality as replacement pureapi with rest=jobid and rest=check functions.

SLiMParser REST Output formats

Run with &rest=docs for program documentation and options. A plain text version is accessed with &rest=help.
&rest=OUTFMT can be used to retrieve individual parts of the output, matching the tabs in the default
(&rest=format) output. Individual OUTFMT elements can also be parsed from the full (&rest=full) server output,
which is formatted as follows:

###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~###
# OUTFMT:
... contents for OUTFMT section ...

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Available REST Outputs

There is currently no specific help available on REST output for this program.