Mercurial > repos > rmarenco > hubarchivecreator

comparison TrackHub.py @ 29:7e8a8b732db3 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
author yating-l
date Wed, 16 May 2018 18:04:20 -0400
parents d786bca6a75d
children
comparison
equal deleted inserted replaced
28:6aa28a85cc38 29:7e8a8b732db3
4 import logging 4 import logging
5 import os 5 import os
6 import tempfile 6 import tempfile
7 import shutil 7 import shutil
8 import zipfile 8 import zipfile
9 from mako.lookup import TemplateLookup
9 10
10 # Internal dependencies 11 # Internal dependencies
11 from Datatype import Datatype 12 from datatypes.Datatype import Datatype
12 from util import subtools 13 from util import subtools
13 14 from util import santitizer
14 from mako.lookup import TemplateLookup 15
16
15 17
16 18
17 class TrackHub(object): 19 class TrackHub(object):
18 """docstring for TrackHub""" 20 """docstring for TrackHub"""
19 21
20 def __init__(self, inputFastaFile, user_email, outputFile, extra_files_path, tool_directory): 22 def __init__(self, inputFastaFile, user_email, outputFile, extra_files_path, tool_directory):
21 super(TrackHub, self).__init__() 23 super(TrackHub, self).__init__()
22
23 self.rootAssemblyHub = None 24 self.rootAssemblyHub = None
24 25
25 self.mySpecieFolderPath = None 26 self.mySpecieFolderPath = None
26 self.myTracksFolderPath = None 27 self.myTracksFolderPath = None
27 self.tool_directory = tool_directory 28 self.tool_directory = tool_directory
66 67
67 # Init the Datatype 68 # Init the Datatype
68 Datatype.pre_init(self.reference_genome, self.two_bit_final_path, self.chromSizesFile, 69 Datatype.pre_init(self.reference_genome, self.two_bit_final_path, self.chromSizesFile,
69 self.extra_files_path, self.tool_directory, 70 self.extra_files_path, self.tool_directory,
70 self.mySpecieFolderPath, self.myTracksFolderPath) 71 self.mySpecieFolderPath, self.myTracksFolderPath)
71 72 '''
72 def createZip(self): 73 def createZip(self):
73 for root, dirs, files in os.walk(self.rootAssemblyHub): 74 for root, dirs, files in os.walk(self.rootAssemblyHub):
74 # Get all files and construct the dir at the same time 75 # Get all files and construct the dir at the same time
75 for file in files: 76 for file in files:
76 self.outputZip.write(os.path.join(root, file)) 77 self.outputZip.write(os.path.join(root, file))
77 78
78 self.outputZip.close() 79 self.outputZip.close()
79 80 '''
80 def addTrack(self, trackDbObject=None): 81 def addTrack(self, trackDbObject=None):
81 # Create the trackDb.txt file in the specie folder, if not exists 82 # Create the trackDb.txt file in the specie folder, if not exists
82 # Else append the new track 83 # Else append the new track
83 # TODO: Get this out of the function 84 # TODO: Get this out of the function
84 trackDbTxtFilePath = os.path.join(self.mySpecieFolderPath, 'trackDb.txt') 85 trackDbTxtFilePath = os.path.join(self.mySpecieFolderPath, 'trackDb.txt')
85
86 # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object 86 # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object
87 with open(trackDbTxtFilePath, 'a+') as trackDbFile: 87 with open(trackDbTxtFilePath, 'a+') as trackDbFile:
88 group_name = trackDbObject["group"]
89 trackDbObject["group"] = santitizer.sanitize_group_name(trackDbObject["group"])
88 trackDbs = [trackDbObject] 90 trackDbs = [trackDbObject]
89
90 # TODO: The addGroup does not belong here. Move it when the group becomes more than just a label 91 # TODO: The addGroup does not belong here. Move it when the group becomes more than just a label
91 # Add the group as well, if exists in trackDbObject 92 # Add the group as well, if exists in trackDbObject
92 self.addGroup(trackDbObject.group_name) 93 self.addGroup(group_name)
93 94
94 htmlMakoRendered = self.trackDbTemplate.render( 95 htmlMakoRendered = self.trackDbTemplate.render(
95 trackDbs=trackDbs 96 trackDbs=trackDbs
96 ) 97 )
97 trackDbFile.write(htmlMakoRendered) 98 trackDbFile.write(htmlMakoRendered)
98 99
99 logging.debug("We just added track {0} (in group {1})".format(trackDbObject.trackName, 100 #logging.debug("We just added track {0} (in group {1})".format(trackDbObject.trackName,
100 trackDbObject.group_name.lower().replace(' ', '_'))) 101 # trackDbObject.group_name.lower().replace(' ', '_')))
101 102 logging.debug("We just added track {0} (in group {1})".format(trackDbObject.get("track"),
103 trackDbObject.get("group").lower().replace(' ', '_')))
102 def addGroup(self, group_name="Default"): 104 def addGroup(self, group_name="Default"):
103 # If not already present in self.groups, add to groups.txt 105 # If not already present in self.groups, add to groups.txt
104 # Create the trackDb.txt file in the specie folder, if not exists 106 # Create the trackDb.txt file in the specie folder, if not exists
105 # Else append the new track 107 # Else append the new track
106 # TODO: Get this out of the function 108 # TODO: Get this out of the function
166 htmlMakoRendered = mytemplate.render( 168 htmlMakoRendered = mytemplate.render(
167 walkable_tree=walkable_tree 169 walkable_tree=walkable_tree
168 ) 170 )
169 htmlOutput.write(htmlMakoRendered) 171 htmlOutput.write(htmlMakoRendered)
170 172
173
171 def __createAssemblyHub__(self, extra_files_path): 174 def __createAssemblyHub__(self, extra_files_path):
172 # Get all necessaries infos first 175 # Get all necessaries infos first
173 # 2bit file creation from input fasta 176 # 2bit file creation from input fasta
174 177
175 # baseNameFasta = os.path.basename(fasta_file_name) 178 # baseNameFasta = os.path.basename(fasta_file_name)