def exec_before_job( app, inp_data, out_data, param_dict, tool=None): """Build a temp file with errors in it""" errors = [] for name, data in inp_data.items(): validation_errors = data.validation_errors for error in validation_errors: # build dummy class try: temp = eval(error.err_type)() except: temp = object() # stuff attributes temp.__dict__ = util.string_to_object( error.attributes ) errors.append(temp) # There *should* only be 1 input, so we assume there is and continue # base64 pickel errors_str = util.object_to_string( errors ) # write database_tmp = "./database/tmp" # globaly visible path error_file = tempfile.NamedTemporaryFile(mode="w", dir=database_tmp, suffix=".b64") error_file_name = error_file.name error_file.close() error_file = open(error_file_name, "w") error_file.write(errors_str) error_file.close() param_dict["errorsfile"] = error_file_name
def index(self, trans, init=False, **kwd): base_url = None params = dict(kwd) try: store = params.get("__GALAXY__", None) if store: store = json.loads(util.string_to_object(store)) else: store = {} UCSC_URL = 'UCSC_URL' base_url = store.get(UCSC_URL, "http://genome.ucsc.edu/cgi-bin/hgTables?") params = dict(kwd) params['init'] = init if not init: for key, value in kwd.items(): store[key] = value try: del store["__GALAXY__"] except: pass else: store = {} if init == "1": base_url = "http://genome.ucsc.edu/cgi-bin/hgTables?" params['db'] = 'hg17' if init == "2": base_url = "http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?" params['db'] = 'hg17' if init == "3": base_url = "http://archaea.ucsc.edu/cgi-bin/hgTables?" store[UCSC_URL] = base_url try: del params["__GALAXY__"] except: pass url = base_url + urllib.urlencode(params) page = urllib.urlopen(url) content = page.info().get('Content-type', '') except Exception, exc: trans.log_event("Proxy Error -> %s" % str(exc)) msg = 'There has been a problem connecting to <i>%s</i> <p> <b>%s<b>' % ( base_url, exc) return msg
def index(self, trans, init=False, **kwd): base_url = None params = dict(kwd) try: store = params.get("__GALAXY__", None) if store: store = json.loads(util.string_to_object(store)) else: store = {} UCSC_URL = 'UCSC_URL' base_url = store.get(UCSC_URL, "http://genome.ucsc.edu/cgi-bin/hgTables?") params = dict(kwd) params['init'] = init if not init: for key, value in kwd.items(): store[key] = value try: del store["__GALAXY__"] except: pass else: store = {} if init == "1": base_url = "http://genome.ucsc.edu/cgi-bin/hgTables?" params['db'] = 'hg17' if init == "2": base_url = "http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?" params['db'] = 'hg17' if init == "3": base_url = "http://archaea.ucsc.edu/cgi-bin/hgTables?" store[UCSC_URL] = base_url try: del params["__GALAXY__"] except: pass url = base_url + urllib.urlencode(params) page = urllib.urlopen(url) content = page.info().get('Content-type', '') except Exception, exc: trans.log_event( "Proxy Error -> %s" % str(exc) ) msg = 'There has been a problem connecting to <i>%s</i> <p> <b>%s<b>' % (base_url, exc) return msg
def main(): options, args = doc_optparse.parse( __doc__ ) try: extension = options.ext except: doc_optparse.exception() # create datatype data = model.Dataset( extension=extension, id=int( args[0] ) ) data.file_path = "/home/ian/trunk/database/files/" if options.metadata: data.metadata = util.string_to_object( options.metadata ) errors = data.datatype.validate( data ) print util.object_to_string(errors)
def main(): options, args = doc_optparse.parse(__doc__) methods = [] try: if options.methods: methods = options.methods.split(",") except: pass ext = options.ext in_file = open(args[0], "r") error_file = open(args[1], "r") out_file = open(args[2], "w") # string_to_object errors error_list = util.string_to_object(error_file.read()) # index by error type and then by line number error_lines = {} error_types = {} for error in error_list: if error.linenum: if error.linenum in error_lines: error_lines[error.linenum].append(error) else: error_lines[error.linenum] = [error] error_type = error.__class__.__name__ if error_type in error_types: error_types[error_type].append(error) else: error_types[error_type] = [error] linenum = 0 for line in in_file: linenum += 1 # write unless if "lines" in methods: if linenum in error_lines: line = None # other processing here? if line: out_file.write(line)
def main(): options, args = doc_optparse.parse( __doc__ ) methods = [] try: if options.methods: methods = options.methods.split(",") except: pass ext = options.ext in_file = open(args[0], "r") error_file = open(args[1], "r") out_file = open(args[2], "w") # string_to_object errors error_list = util.string_to_object(error_file.read()) # index by error type and then by line number error_lines = {} error_types = {} for error in error_list: if error.linenum: if error.linenum in error_lines: error_lines[error.linenum].append(error) else: error_lines[error.linenum] = [error] error_type = error.__class__.__name__ if error_type in error_types: error_types[error_type].append(error) else: error_types[error_type] = [error] linenum = 0 for line in in_file: linenum += 1 # write unless if "lines" in methods: if linenum in error_lines: line = None # other processing here? if line: out_file.write(line)
def __string_to_state(self, state_string): encoded_state = string_to_object(state_string) state = DefaultToolState() state.decode(encoded_state, self.tool, self.app) return state
def __string_to_state( self, state_string ): encoded_state = string_to_object( state_string ) state = DefaultToolState() state.decode( encoded_state, self.tool, self.app ) return state