Mercurial > repos > yating-l > hubarchivecreator

--- a/Reader.py	Tue Sep 26 17:56:42 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,117 +0,0 @@
-import json
-import logging
-import codecs
-
-
-# Internal dependencies
-from datatypes.binary.Bam import Bam
-from datatypes.binary.BigWig import BigWig
-from datatypes.binary.BigBed import BigBed
-from datatypes.interval.Bed import Bed
-from datatypes.interval.BedSimpleRepeats import BedSimpleRepeats
-from datatypes.interval.BedSpliceJunctions import BedSpliceJunctions
-from datatypes.interval.CytoBand import CytoBand
-from datatypes.interval.BedBlatAlignments import BedBlatAlignments
-from datatypes.interval.BedBlastAlignments import BedBlastAlignments
-from datatypes.interval.Gff3 import Gff3
-from datatypes.interval.Gtf import Gtf
-from datatypes.interval.Psl import Psl
-from datatypes.sequence.Fasta import Fasta
-from util import santitizer
-
-class Reader(object):
-
-    DATATYPE_CLASS = [Bam, BigWig, BigBed, Bed, BedSimpleRepeats, BedSpliceJunctions, CytoBand, BedBlatAlignments, BedBlastAlignments, Gff3, Gtf, Psl, Fasta]
-
-    def __init__(self, input_json_file):
-        self.inputFile = input_json_file
-        self.args = self.loadJson()
-
-
-    def loadJson(self):
-        try:
-            data_file = codecs.open(self.inputFile, 'r', 'utf-8')
-            return json.load(data_file)
-        except IOError:
-            print "Cannot find JSON file\n"
-            exit(1)
-
-    def getToolDir(self):
-        try:
-            return self.args["tool_directory"]
-        except KeyError:
-            print ("tool_directory is not defined in the input file!")
-            exit(1)
-
-    def getExtFilesPath(self):
-        try:
-            return self.args["extra_files_path"]
-        except KeyError:
-            print ("extra_files_path is not defined in the input file!")
-            exit(1)
-
-    def getUserEmail(self):
-        try:
-            return self.args["user_email"]
-        except KeyError:
-            print ("user_email is not defined in the input file!")
-            exit(1)
-
-    def getDebugMode(self):
-        try:
-            return self.args["debug_mode"]
-        except KeyError:
-            print ("debug_mode is not defined in the input file!")
-            exit(1)
-
-
-    def getRefGenome(self):
-        array_inputs_reference_genome = self.args["fasta"]
-        # TODO: Replace these with the object Fasta
-        input_fasta_file = array_inputs_reference_genome["false_path"]
-        input_fasta_file_name = santitizer.sanitize_name_input(array_inputs_reference_genome["name"])
-        genome_name = santitizer.sanitize_name_input(self.args["genome_name"])
-        reference_genome = Fasta(input_fasta_file,
-                             input_fasta_file_name, genome_name)
-        return reference_genome
-
-
-    def getTracksData(self):
-        self.logger = logging.getLogger(__name__)
-        all_datatype_dictionary = dict()
-        for datatype in self.DATATYPE_CLASS:
-            class_name = datatype.__name__
-            array_inputs = self.args.get(str(class_name))
-            if array_inputs:
-                self.logger.debug("Create %s objects\n", class_name)
-                self.logger.debug("array_inputs: %s", array_inputs)
-                all_datatype_dictionary.update(self.create_ordered_datatype_objects(datatype, array_inputs))
-
-        return all_datatype_dictionary
-
-    def create_ordered_datatype_objects(self, ExtensionClass, array_inputs):
-        """
-        Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
-        and update the dictionary of datatype
-
-        :param ExtensionClass:
-        :param array_inputs:
-        :type ExtensionClass: Datatype
-        :type array_inputs: list[string]
-        """
-
-        datatype_dictionary = {}
-
-        # TODO: Optimize this double loop
-        for input_data in array_inputs:
-            input_false_path = input_data["false_path"]
-            santitizer.sanitize_name_input(input_data["name"])
-            extensionObject = ExtensionClass(input_false_path, input_data)
-            extensionObject.generateCustomTrack()
-            datatype_dictionary.update({input_data["order_index"]: extensionObject})
-        return datatype_dictionary
-
-
-
-
-
--- a/TrackDb.py	Tue Sep 26 17:56:42 2017 -0400
+++ b/TrackDb.py	Tue Sep 26 18:46:02 2017 -0400
@@ -67,8 +67,8 @@
         if not "color" in extraSettings:
             extraSettings["color"] = "#000000"
         extraSettings["color"] = TrackDb.getRgb(extraSettings["color"])
-        if not "group" in extraSettings:
-            extraSettings["group"] = "Default group"
+        #if "group" in extraSettings:
+            #extraSettings["group"] = santitizer.sanitize_group_name(extraSettings["group"])
         if not "thickDrawItem" in extraSettings:
             extraSettings["thickDrawItem"] = "off"
--- a/TrackHub.py	Tue Sep 26 17:56:42 2017 -0400
+++ b/TrackHub.py	Tue Sep 26 18:46:02 2017 -0400
@@ -11,6 +11,7 @@
 # Internal dependencies
 from datatypes.Datatype import Datatype
 from util import subtools
+from util import santitizer


@@ -84,11 +85,12 @@
         trackDbTxtFilePath = os.path.join(self.mySpecieFolderPath, 'trackDb.txt')
         # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object
         with open(trackDbTxtFilePath, 'a+') as trackDbFile:
+            group_name = trackDbObject["group"]
+            trackDbObject["group"] = santitizer.sanitize_group_name(trackDbObject["group"])
             trackDbs = [trackDbObject]
-
             # TODO: The addGroup does not belong here. Move it when the group becomes more than just a label
             # Add the group as well, if exists in trackDbObject
-            self.addGroup(trackDbObject["group"])
+            self.addGroup(group_name)

             htmlMakoRendered = self.trackDbTemplate.render(
                 trackDbs=trackDbs
--- a/hubArchiveCreator.xml	Tue Sep 26 17:56:42 2017 -0400
+++ b/hubArchiveCreator.xml	Tue Sep 26 18:46:02 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.4.2">
+<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.5.0">
     <description>
         This Galaxy tool permits to prepare your files to be ready for
         Assembly Hub visualization.
--- a/util/Reader.py	Tue Sep 26 17:56:42 2017 -0400
+++ b/util/Reader.py	Tue Sep 26 18:46:02 2017 -0400
@@ -105,6 +105,7 @@
         # TODO: Optimize this double loop
         for input_data in array_inputs:
             input_false_path = input_data["false_path"]
+            input_data["name"] = santitizer.sanitize_name_input(input_data["name"])
             extensionObject = ExtensionClass(input_false_path, input_data)
             extensionObject.generateCustomTrack()
             datatype_dictionary.update({input_data["order_index"]: extensionObject})
--- a/util/santitizer.py	Tue Sep 26 17:56:42 2017 -0400
+++ b/util/santitizer.py	Tue Sep 26 18:46:02 2017 -0400
@@ -45,7 +45,6 @@
             .replace("/", "_") \
             .replace(" ", "_")

-
 def sanitize_name_inputs(inputs_data):
     """
     Sanitize value of the keys "name" of the dictionary passed in parameter.
@@ -57,3 +56,6 @@
     """
     for key in inputs_data:
         inputs_data[key]["name"] = sanitize_name_input(inputs_data[key]["name"])
+
+def sanitize_group_name(group_name):
+    return group_name.lower().replace(' ', '_')