--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TrackHub.py	Wed Apr 12 17:41:55 2017 -0400
@@ -0,0 +1,192 @@
+#!/usr/bin/env python
+
+import os
+import subprocess
+import shutil
+import json
+import utils
+
+
+class TrackHub:
+    def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path, metaData, jbrowse_host):
+        self.input_files = inputFiles.tracks
+        self.outfile = outputDirect
+        self.outfolder = extra_files_path
+        self.out_path = os.path.join(extra_files_path, genome)
+        self.reference = reference
+        self.tool_dir = tool_dir
+        self.metaData = metaData
+        self.raw = os.path.join(self.out_path, 'raw')
+        self.json = os.path.join(self.out_path, 'json')
+        self.jbrowse_host = jbrowse_host
+        try: 
+            if os.path.exists(self.json):
+                shutil.rmtree(self.json)
+            os.makedirs(self.json)
+        except OSError as e:
+            print "Cannot create json folder error({0}): {1}".format(e.errno, e.strerror)
+        else:
+            print "Create jbrowse folder {}".format(self.out_path)
+    
+    def createHub(self):
+        self.prepareRefseq()
+        for input_file in self.input_files:
+            self.addTrack(input_file)
+        self.indexName()
+        slink = self.makeArchive()
+        self.outHtml(slink)
+        print "Success!\n"
+    
+    def prepareRefseq(self):
+        try:
+            #print os.path.join(self.tool_dir, 'prepare-refseqs.pl') + ", '--fasta', " + self.reference +", '--out', self.json])"
+            subprocess.call(['prepare-refseqs.pl', '--fasta', self.reference, '--out', self.json])
+        except OSError as e:
+            print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror)
+    #TODO: hard coded the bam and bigwig tracks. Need to allow users to customize the settings
+    def addTrack(self, track):
+        #print "false_path" , track['false_path']
+        if track['false_path'] in self.metaData.keys():
+            metadata = self.metaData[track['false_path']]
+        else:
+            metadata = {}
+        self.SetMetadata(track, metadata)
+        if track['dataType'] == 'bam':
+            self.Bam(track, metadata)
+           # print "add bam track\n"
+        elif track['dataType'] == 'bigwig':
+            self.BigWig(track, metadata)
+        else: 
+            flat_file = os.path.join(self.raw, track['fileName'])
+            if track['dataType'] == 'bed':
+                subprocess.call(['flatfile-to-json.pl', '--bed', flat_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
+            elif track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf' or track['dataType'] == 'blastxml':
+                subprocess.call(['flatfile-to-json.pl', '--gff', flat_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"glyph": "JBrowse/View/FeatureGlyph/Segments", "category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
+            elif track['dataType'] == 'gff3_transcript':
+                subprocess.call(['flatfile-to-json.pl', '--gff', flat_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"transcriptType": "transcript", "category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
+            else:
+                subprocess.call(['flatfile-to-json.pl', '--gff', flat_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
+            
+    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)
+        slink = source.replace('/', '_')
+        slink = os.path.join('/var/www/html/JBrowse-1.12.1/data', slink)
+        try:
+            if os.path.islink(slink):
+                os.unlink(slink)
+        except OSError as oserror:
+            print "Cannot create symlink to the data({0}): {1}".format(oserror.errno, oserror.strerror)
+        os.symlink(source, slink)
+        return slink
+        '''
+        data_folder = '/gonramp/static/JBrowse-1.12.1/jbrowse_hub'
+        try:
+            if os.path.exists(data_folder):
+                if os.path.isdir(data_folder):
+                    shutil.rmtree(data_folder)
+                else:
+                    os.remove(data_folder)
+        except OSError as oserror:
+            print "Cannot create data folder({0}): {1}".format(oserror.errno, oserror.strerror)
+        shutil.copytree(self.out_path, data_folder)
+        subprocess.call(['chmod', '-R', 'o+rx', '/var/www/html/JBrowse-1.12.1/jbrowse_hub'])
+        shutil.rmtree(self.out_path)
+        '''
+    
+    #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)
+
+    def createTrackList(self):
+        trackList = os.path.join(self.json, "trackList.json")
+        if not os.path.exists(trackList):
+            os.mknod(trackList)
+    
+    def Bam(self, track, metadata):
+        #create trackList.json if not exist
+        self.createTrackList()
+        json_file = os.path.join(self.json, "trackList.json")
+        bam_track = dict()
+        bam_track['type'] = 'JBrowse/View/Track/Alignments2'
+        bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM'
+        bam_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
+        bam_track['baiUrlTemplate'] = os.path.join('../raw', track['index'])
+        bam_track['label'] = metadata['label']
+        bam_track['category'] = metadata['category']
+        bam_track = json.dumps(bam_track)
+        #Use add-track-json.pl to add bam track to json file
+        new_track = subprocess.Popen(['echo', bam_track], stdout=subprocess.PIPE)
+        subprocess.call(['add-track-json.pl', json_file], stdin=new_track.stdout)
+    
+    def BigWig(self, track, metadata):
+        #create trackList.json if not exist
+        self.createTrackList()
+        json_file = os.path.join(self.json, "trackList.json")
+        bigwig_track = dict()
+        bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
+        bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
+        bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig'
+        bigwig_track['label'] = metadata['label']
+        bigwig_track['style'] = metadata['style']
+        bigwig_track['category'] = metadata['category']
+        bigwig_track = json.dumps(bigwig_track)
+        #Use add-track-json.pl to add bigwig track to json file
+        new_track = subprocess.Popen(['echo', bigwig_track], stdout=subprocess.PIPE)
+        #output = new_track.communicate()[0]
+        subprocess.call(['add-track-json.pl', json_file], stdin=new_track.stdout)
+
+    #If the metadata is not set, use the default value
+    def SetMetadata(self, track, metadata):
+        if 'label' not in metadata.keys() or metadata['label'] == '':
+            metadata['label'] = track['fileName']
+        if 'color' not in metadata.keys() or metadata['color'] == '':
+            metadata['color'] = "#daa520"
+        if track['dataType'] == 'bigwig':
+            if 'style' not in metadata.keys():
+                metadata['style'] = {}
+            if 'pos_color' not in metadata['style'] or metadata['style']['pos_color'] == '':
+                metadata['style']['pos_color'] = "#FFA600"
+            if 'neg_color' not in metadata['style'] or metadata['style']['neg_color'] == '':
+                metadata['style']['neg_color'] = "#005EFF"
+        if 'category' not in metadata.keys() or metadata['category'] == '':
+            metadata['category'] = "Default group"
+        if track['dataType'] == 'blastxml':
+            metadata['type'] = "G-OnRamp_plugin/BlastAlignment"
+        elif track['dataType'] == 'gff3_transcript' or track['dataType'] == 'gff3_mrna':
+            metadata['type'] = "G-OnRamp_plugin/GenePred"
+        else:
+            metadata['type'] = "CanvasFeatures"
+
+
+
+   
+
+
+