Sharg Script

gistfile1.txt

import os
from mod_python import apache

#   -  make sure file in subfolder 'resources/versions.txt' exists
#   -  URI passed to script is formated like: check/RESOURCENAME
#   -  RESOURCENAME is formated as either: 
#      * 'SeqAn_Linux_64_Alf_2.0.0' (Argument Parser in Seqan 2) 
#      * 'SeqAn3_Linux_64_Raptor_2.0.0' (Argument Parser in Seqan 3) 
#      * 'SeqAn-Sharg_Linux_64_Alf_2.0.0' (Stand alone Sharg Parser) 
#   The toolname of a request is extracted and the returned by the server.

def handler( req ):
    resource_database = {'SeqAn_REST_TEST': 'true'}
    script_path = os.path.dirname(os.path.realpath(__file__))

    # load resource file
    fname = script_path + '/resources/seqan_versions.txt'
    if not os.path.isfile(fname):
      req.log_error("[VERSION CHECK ERROR] The resource file /check/resources/seqan_versions.txt cannot be found!")
      raise apache.SERVER_RETURN, apache.HTTP_NOT_FOUND

    lines = [line.strip() for line in open(fname, 'r')]
    for line in lines:
      fields = line.split("\t")
      if len(fields) == 2:
        resource_database[fields[0]] = fields[1]
      else:
        req.log_error("[VERSION CHECK ERROR] Mal formed resource file!")

    # Extract the resource name
    uripath = [p for p in req.uri.split('/') if p]

    if len(uripath) != 3 or uripath[0] != 'check' or uripath[1] != 'check.py':
      req.log_error("[VERSION CHECK ERROR] malformed URI path!")
      raise apache.SERVER_RETURN, apache.HTTP_NOT_FOUND
    resource_name = uripath[-1]

    req.log_error(req.filename)

    # return resource
    if req.method == 'GET':
        req.content_type = 'application/octet-stream'

        # for debugging: if 'all' is provided as resource name print all entries
        if resource_name == 'all':
            content = resource_database
            req.write(str(content))
            return apache.OK
        #now we have a proper resource string like: 'SeqAn3_Linux_64_Raptor_2.0.0'
        fields = resource_name.split('_')

        # sanity check for number of fields and prefix
        if len(fields) == 1:
           raise apache.SERVER_RETURN, apache.HTTP_NOT_FOUND

        if not 'SeqAn' in fields[0]:
           req.log_error("[VERSION CHECK ERROR] SeqAn prefix missing in request string!")
           raise apache.SERVER_RETURN, apache.HTTP_NOT_FOUND

        tool_name = "_".join(fields[3:-1]) # in case the app name had contained '_'

        seqan = "seqan"
        if 'SeqAn3' in fields[0]:
           seqan = "seqan3"
        elif 'Sharg' in fields[0]:
           seqan = "sharg"

        # retrieve previously stored resource
        if tool_name in resource_database:
           req.write(resource_database[tool_name] + os.linesep + resource_database[seqan])
        else:
           req.write("UNREGISTERED_APP" + os.linesep + resource_database[seqan])

        # store full request string in apache log (also stores ip and date)
        req.log_error(resource_name)
        return apache.OK
    else:
        raise apache.SERVER_RETURN, apache.HTTP_METHOD_NOT_ALLOWED

    return apache.OK