Mercurial > repos > rmarenco > hubarchivecreator

comparison TrackHub.py @ 17:c02720d1afee draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
author rmarenco
date Fri, 30 Sep 2016 15:14:24 -0400
parents 3233451a3bd6
children d786bca6a75d
comparison
equal deleted inserted replaced
16:3233451a3bd6 17:c02720d1afee
31 self.genome_name = inputFastaFile.assembly_id 31 self.genome_name = inputFastaFile.assembly_id
32 self.specie_html = self.genome_name + '.html' 32 self.specie_html = self.genome_name + '.html'
33 self.default_pos = None 33 self.default_pos = None
34 self.user_email = user_email 34 self.user_email = user_email
35 35
36 # Set containing the groups already added. Updated by addGroup()
37 self.groups = set()
38
36 # TODO: Modify according to the files passed in parameter 39 # TODO: Modify according to the files passed in parameter
40 # ---- Templates ----
41 # Template trackDb
37 mylookup = TemplateLookup(directories=[os.path.join(tool_directory, 'templates/trackDb')], 42 mylookup = TemplateLookup(directories=[os.path.join(tool_directory, 'templates/trackDb')],
38 output_encoding='utf-8', encoding_errors='replace') 43 output_encoding='utf-8', encoding_errors='replace')
39 self.trackDbTemplate = mylookup.get_template("layout.txt") 44 self.trackDbTemplate = mylookup.get_template("layout.txt")
45
46 # Template groups
47 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates/groupsTxt')],
48 output_encoding='utf-8', encoding_errors='replace')
49 self.groupsTemplate = mylookup.get_template("layout.txt")
50
51 # ---- End Templates ----
40 52
41 self.extra_files_path = extra_files_path 53 self.extra_files_path = extra_files_path
42 self.outputFile = outputFile 54 self.outputFile = outputFile
43 55
44 # Create the structure of the Assembly Hub 56 # Create the structure of the Assembly Hub
66 self.outputZip.close() 78 self.outputZip.close()
67 79
68 def addTrack(self, trackDbObject=None): 80 def addTrack(self, trackDbObject=None):
69 # Create the trackDb.txt file in the specie folder, if not exists 81 # Create the trackDb.txt file in the specie folder, if not exists
70 # Else append the new track 82 # Else append the new track
83 # TODO: Get this out of the function
71 trackDbTxtFilePath = os.path.join(self.mySpecieFolderPath, 'trackDb.txt') 84 trackDbTxtFilePath = os.path.join(self.mySpecieFolderPath, 'trackDb.txt')
72 85
73 # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object 86 # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object
74 with open(trackDbTxtFilePath, 'a+') as trackDbFile: 87 with open(trackDbTxtFilePath, 'a+') as trackDbFile:
75 trackDbs = [trackDbObject] 88 trackDbs = [trackDbObject]
89
90 # 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 self.addGroup(trackDbObject.group_name)
93
76 htmlMakoRendered = self.trackDbTemplate.render( 94 htmlMakoRendered = self.trackDbTemplate.render(
77 trackDbs=trackDbs 95 trackDbs=trackDbs
78 ) 96 )
79 trackDbFile.write(htmlMakoRendered) 97 trackDbFile.write(htmlMakoRendered)
98
99 def addGroup(self, group_name="Default"):
100 # If not already present in self.groups, add to groups.txt
101 # Create the trackDb.txt file in the specie folder, if not exists
102 # Else append the new track
103 # TODO: Get this out of the function
104 groupsTxtFilePath = os.path.join(self.mySpecieFolderPath, 'groups.txt')
105
106 # If the group is already present, we don't need to add it
107 if group_name in self.groups:
108 return
109
110 # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object
111 with open(groupsTxtFilePath, 'a+') as groupFile:
112 # Add the group as well, if exists in trackDbObject
113
114 htmlMakoRendered = self.groupsTemplate.render(
115 label=group_name
116 )
117 groupFile.write(htmlMakoRendered)
118 self.groups.add(group_name)
80 119
81 def terminate(self): 120 def terminate(self):
82 # Just a test to output a simple HTML 121 # Just a test to output a simple HTML
83 # TODO: Create a class to handle the file object 122 # TODO: Create a class to handle the file object
84 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')], 123 mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
180 descriptionHtmlFilePath = os.path.join(mySpecieFolderPath, 'description.html') 219 descriptionHtmlFilePath = os.path.join(mySpecieFolderPath, 'description.html')
181 self.__fillDescriptionHtmlFile__(descriptionHtmlFilePath) 220 self.__fillDescriptionHtmlFile__(descriptionHtmlFilePath)
182 221
183 # Create the file groups.txt 222 # Create the file groups.txt
184 # TODO: If not inputs for this, do no create the file 223 # TODO: If not inputs for this, do no create the file
185 groupsTxtFilePath = os.path.join(mySpecieFolderPath, 'groups.txt') 224 # groupsTxtFilePath = os.path.join(mySpecieFolderPath, 'groups.txt')
186 self.__fillGroupsTxtFile__(groupsTxtFilePath) 225 # self.__fillGroupsTxtFile__(groupsTxtFilePath)
187 226
188 # Create the folder tracks into the specie folder 227 # Create the folder tracks into the specie folder
189 tracksFolderPath = os.path.join(mySpecieFolderPath, "tracks") 228 tracksFolderPath = os.path.join(mySpecieFolderPath, "tracks")
190 if not os.path.exists(tracksFolderPath): 229 if not os.path.exists(tracksFolderPath):
191 os.makedirs(tracksFolderPath) 230 os.makedirs(tracksFolderPath)