comparison TrackHub.py @ 3:eda851e52060 draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 479fc6490e24ca0e5034ae6c3579882e97e095e6-dirty

2:25ad6770359e

#!/usr/bin/env python

import os
import subprocess
import shutil
import json
import utils


class TrackHub:

    def indexName(self):
        subprocess.call(['generate-names.pl', '-v', '--out', self.json])
        print "finished name index \n"

    def makeArchive(self):
        shutil.make_archive(self.out_path, 'zip', self.out_path)
        file_dir = os.path.abspath(self.outfile)
        source_dir = os.path.dirname(file_dir)
        folder_name = os.path.basename(self.outfolder)
        source_name = os.path.basename(self.out_path)
        source = os.path.join(source_dir, folder_name, source_name)

        except OSError as oserror:
            print "Cannot create symlink to the data({0}): {1}".format(oserror.errno, oserror.strerror)
        os.symlink(source, slink)
        return slink
    
    #TODO: this will list all zip files in the filedir and sub-dirs. worked in Galaxy but all list zip files in test-data when
    #run it locally. May need modify
    def outHtml(self, slink):
        with open(self.outfile, 'w') as htmlfile:
            htmlstr = 'The JBrowse Hub is created: <br>'
            zipfiles = '<li><a href = "%s">Download</a></li>'
            url = self.jbrowse_host + "/JBrowse-1.12.1/index.html?data=%s"
            jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub</a></li>' % url
            filedir_abs = os.path.abspath(self.outfile)
            filedir = os.path.dirname(filedir_abs)
            filedir = os.path.join(filedir, self.outfolder)
            for root, dirs, files in os.walk(filedir):
                for file in files:
                    if file.endswith('.zip'):   
                        relative_directory = os.path.relpath(root, filedir)
                        relative_file_path = os.path.join(relative_directory, file)
                        htmlstr += zipfiles % relative_file_path
            link_name = os.path.basename(slink)
            relative_path = os.path.join('data', link_name + '/json')
            htmlstr += jbrowse_hub % relative_path
            htmlfile.write(htmlstr)

3:eda851e52060

#!/usr/bin/env python

import os
import subprocess
import shutil
import zipfile
import json
import utils


class TrackHub:

    def indexName(self):
        subprocess.call(['generate-names.pl', '-v', '--out', self.json])
        print "finished name index \n"

    def makeArchive(self):
        file_dir = os.path.abspath(self.outfile)
        source_dir = os.path.dirname(file_dir)
        folder_name = os.path.basename(self.outfolder)
        source_name = os.path.basename(self.out_path)
        source = os.path.join(source_dir, folder_name, source_name)

        except OSError as oserror:
            print "Cannot create symlink to the data({0}): {1}".format(oserror.errno, oserror.strerror)
        os.symlink(source, slink)
        return slink
    
    def outHtml(self, slink):
        with open(self.outfile, 'w') as htmlfile:
            htmlstr = 'The JBrowse Hub is created: <br>'
            url = self.jbrowse_host + "/JBrowse-1.12.1/index.html?data=%s"
            jbrowse_hub = '<li><a href = "%s" target="_blank">View JBrowse Hub</a></li>' % url
            link_name = os.path.basename(slink)
            relative_path = os.path.join('data', link_name + '/json')
            htmlstr += jbrowse_hub % relative_path
            htmlfile.write(htmlstr)