view util/Reader.py @ 0:bc00f5c4c59e draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git

import json
import re
import logging
import codecs
from apollo.ApolloUser import ApolloUser
from util import santitizer 

class Reader(object):

    def __init__(self, input_json_file):
        self.inputFile = input_json_file
        self.args = self.loadJson()
        
    
    def loadJson(self):
        try:
            data_file = codecs.open(self.inputFile, 'r', 'utf-8')   
            return json.load(data_file) 
        except IOError:
            print "Cannot find JSON file\n"
            exit(1)

    def getJBrowseHubDir(self):
        try:
            return self.args["jbrowse_hub"]
        except KeyError:
            print ("jbrowse_hub is not defined in the input file!")
            exit(1)

    def getToolDir(self):
        try:
            return self.args["tool_directory"]
        except KeyError:
            print ("tool_directory is not defined in the input file!")
            exit(1)

    def getExtFilesPath(self):
        try:
            return self.args["extra_files_path"]
        except KeyError:
            print ("extra_files_path is not defined in the input file!")
            exit(1)

    def getUserEmail(self):
        try:
            return self.args["user_email"]
        except KeyError:
            print ("user_email is not defined in the input file!")
            exit(1)
    
    def getDebugMode(self):
        try:
            return self.args["debug_mode"]
        except KeyError:
            print ("debug_mode is not defined in the input file!")
            exit(1)
    
    def getApolloHost(self):
        apollo_host = self.args.get("apollo_host")
        return apollo_host
        
        
    def getSpeciesName(self):
        species_name = santitizer.sanitize_name_input(self.args["species_name"])
        return species_name 
        
    def getGenomeName(self):
        jbrowse_hub = self.getJBrowseHubDir()
        with open(jbrowse_hub, 'r') as f:
            html = f.read()
        m = re.search('The new Organism "(.+?)" is created on Apollo', html)
        if m:
            genome_name = m.group(1)
        else:
            print("Cannot find genome name in the jbrowse hub file!")
            exit(1)
        return genome_name
            

    def getApolloUser(self):
        user_info = self.args.get("apollo_user")
        if not user_info:
            firstname = "demo"
            lastname = "user"
            password = "gonramp"
            user_email = self.getUserEmail()
        else:
            firstname = user_info['firstname']
            lastname = user_info['lastname']
            user_email = user_info['user_email']
            password = user_info['password']
        apollo_user = ApolloUser(user_email, firstname, lastname, password)
        return apollo_user