comparison TrackHub.py @ 32:7b955a58d8f2 draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 18da3c5b92673ba5030c24c981c6ca7ebe0bf097-dirty

31:127037c49bc8

import shutil
import zipfile
import json
import tempfile
import logging

from datatypes.Datatype import Datatype
from apollo.ApolloInstance import ApolloInstance
from tracks.TrackStyles import TrackStyles
from util import subtools
from util import santitizer


class TrackHub:
    def __init__(self, inputFastaFile, apollo_user, outputFile, extra_files_path, tool_directory, trackType, apollo_host, user_email):
        
        self.rootAssemblyHub = None

        self.mySpecieFolderPath = None

        self.genome_name = inputFastaFile.assembly_id
        self.extra_files_path = extra_files_path
        self.outputFile = outputFile
        self.chromSizesFile = None

        # Set up apollo
        self.apollo = ApolloInstance(apollo_host, tool_directory, user_email)
        self.apollo_user = apollo_user
        
        # Set all the missing variables of this class, and create physically the folders/files
        self.rootAssemblyHub = self.__createAssemblyHub__(extra_files_path=extra_files_path)
        # Init the Datatype 
        Datatype.pre_init(self.reference_genome, self.chromSizesFile,

    def terminate(self, debug=False):
        """ Write html file """
        self._indexName()
        if not debug:
            self._removeRaw()
        self._makeArchive()
        print "Success!\n"


    def _customizeHTMLFeature(self, trackDbObject):
        if trackDbObject['options']:

    def _indexName(self):
        #subprocess.call(['generate-names.pl', '-v', '--out', self.mySpecieFolderPath])
        subtools.generate_names(self.mySpecieFolderPath)
        print "finished name index \n"

    def _outHtml(self, host_name):
        with open(self.outputFile, 'w') as htmlfile:
            htmlstr = 'The new Organism "%s" is created on Apollo: <br>' % self.genome_name
            jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub on Apollo</a></li>' % host_name
            htmlstr += jbrowse_hub
            htmlfile.write(htmlstr)     

    def _makeArchive(self):
        self.apollo.loadHubToApollo(self.apollo_user, self.genome_name, self.mySpecieFolderPath, admin=True)
        apollo_host = self.apollo.getHost()
        self._outHtml(apollo_host)
        

    def __createAssemblyHub__(self, extra_files_path):
        # Get all necessaries infos first
        # 2bit file creation from input fasta

32:7b955a58d8f2

import shutil
import zipfile
import json
import tempfile
import logging
from mako.lookup import TemplateLookup

from datatypes.Datatype import Datatype
from tracks.TrackStyles import TrackStyles
from util import subtools
from util import santitizer


class TrackHub:
    def __init__(self, inputFastaFile, outputFile, extra_files_path, tool_directory, trackType):
        
        self.rootAssemblyHub = None

        self.mySpecieFolderPath = None

        self.genome_name = inputFastaFile.assembly_id
        self.extra_files_path = extra_files_path
        self.outputFile = outputFile
        self.chromSizesFile = None

        
        # Set all the missing variables of this class, and create physically the folders/files
        self.rootAssemblyHub = self.__createAssemblyHub__(extra_files_path=extra_files_path)
        # Init the Datatype 
        Datatype.pre_init(self.reference_genome, self.chromSizesFile,

    def terminate(self, debug=False):
        """ Write html file """
        self._indexName()
        if not debug:
            self._removeRaw()
        #self._makeArchive()
        self._outHtml()
        print "Success!\n"


    def _customizeHTMLFeature(self, trackDbObject):
        if trackDbObject['options']:

    def _indexName(self):
        #subprocess.call(['generate-names.pl', '-v', '--out', self.mySpecieFolderPath])
        subtools.generate_names(self.mySpecieFolderPath)
        print "finished name index \n"

    def _outHtml(self):
        mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
                                  output_encoding='utf-8', encoding_errors='replace')
        htmlTemplate = mylookup.get_template("display.txt")

        with open(self.outputFile, 'w') as htmlfile:
            htmlMakoRendered = htmlTemplate.render(
            genome_name = self.genome_name,
            trackList = os.path.relpath(self.trackList, self.extra_files_path)
        )
            htmlfile.write(htmlMakoRendered)
        #with open(self.outputFile, 'w') as htmlfile:
        #    htmlstr = 'The new Organism "%s" is created on Apollo: <br>' % self.genome_name
        #    jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub on Apollo</a></li>' % host_name
        #    htmlstr += jbrowse_hub
        #    htmlfile.write(htmlstr)     


    def __createAssemblyHub__(self, extra_files_path):
        # Get all necessaries infos first
        # 2bit file creation from input fasta