# HG changeset patch
# User yating-l
# Date 1509379111 14400
# Node ID fa990284327b532a8ccf6064de20433f89030f6a
# Parent  7486909dfc227cc2e86ae394c6f9ce3ddb1b5cfb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty

diff -r 7486909dfc22 -r fa990284327b datatypes/Datatype.py
--- a/datatypes/Datatype.py	Fri Sep 29 14:50:50 2017 -0400
+++ b/datatypes/Datatype.py	Mon Oct 30 11:58:31 2017 -0400
@@ -96,110 +96,3 @@
     def createTrackDb(self):
         self.track = TrackDb(self.trackName, self.longLabel, self.shortLabel, self.trackDataURL, self.trackType, self.extraSettings)
 
-    
-   
-
-        
-    
-        
-    '''
-    def __init__(self):
-        not_init_message = "The {0} is not initialized." \
-                           "Did you use pre_init static method first?"
-        if Datatype.input_fasta_file is None:
-            raise TypeError(not_init_message.format('reference genome'))
-        if Datatype.extra_files_path is None:
-            raise TypeError(not_init_message.format('track Hub path'))
-        if Datatype.tool_directory is None:
-            raise TypeError(not_init_message.format('tool directory'))
-        self.track = None
-        self.extra_settings = collections.OrderedDict()
-        
-
-    @staticmethod
-    def pre_init(reference_genome, two_bit_path, chrom_sizes_file,
-                 extra_files_path, tool_directory, specie_folder, tracks_folder):
-        Datatype.extra_files_path = extra_files_path
-        Datatype.tool_directory = tool_directory
-
-        # TODO: All this should be in TrackHub and not in Datatype
-        Datatype.mySpecieFolderPath = specie_folder
-        Datatype.myTrackFolderPath = tracks_folder
-
-        Datatype.input_fasta_file = reference_genome
-
-        # 2bit file creation from input fasta
-        Datatype.twoBitFile = two_bit_path
-        Datatype.chromSizesFile = chrom_sizes_file
- 
-    @staticmethod
-    def get_largest_scaffold_name(self):
-        # We can get the biggest scaffold here, with chromSizesFile
-        with open(Datatype.chromSizesFile.name, 'r') as chrom_sizes:
-            # TODO: Check if exists
-            return chrom_sizes.readline().split()[0]
-  
-
-    def createTrack(self, trackName, longLabel, shortLabel, trackDataURL, trackType, extra_settings=None):
-        self.track = TrackDb(trackName, longLabel, shortLabel, trackDataURL, trackType, extra_settings)
-
-    def initRequiredSettings(self, trackSettings, trackDataURL = None, trackType = None):
-        
-        #Initialize required fields: trackName, longLabel, shortLable
-      
-        self.trackSettings = trackSettings
-        self.trackName = self.trackSettings["name"]
-        #self.priority = self.trackSettings["order_index"]
-        #self.track_color = self.trackSettings["track_color"]
-        # TODO: Think about how to avoid repetition of the group_name everywhere
-        #self.group_name = self.trackSettings["group_name"]
-        #self.database = self.trackSettings["database"]
-        if self.trackSettings["long_label"]:
-            self.longLabel = self.trackSettings["long_label"]
-        else:
-            self.longLabel = self.trackName
-        if not "short_label" in self.trackSettings:
-            self.shortLabel = ""
-        else:
-            self.shortLabel = self.trackSettings["short_label"]
-        self.trackDataURL = trackDataURL
-        self.trackType = trackType
-    
-    def setExtLink(self, database, inputFile, seqType=None, useIframe=True, iframeHeight=None, iframeWidth=None):
-        if "NCBI" in database:
-            if not seqType:
-                self.seqType = int(self.getSeqType(inputFile))
-            else:
-                self.seqType = seqType
-            if self.seqType < 0:
-                print self.seqType
-                raise Exception("Sequence Type is not set for bigPsl. Stopping the application")
-            if self.seqType == 2:
-                self.extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/protein/$$"
-            elif self.seqType == 1:
-                self.extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/nuccore/$$"
-            else:
-                raise Exception("Sequence Type {0} is not valid for bigPsl. Stopping the application".format(self.seqType))
-        elif "UniProt" in database:
-            self.extra_settings["url"] = "http://www.uniprot.org/uniprot/$$"
-        elif "FlyBase" in database:
-            self.extra_settings["url"] = "http://flybase.org/reports/$$"
-        else:
-            self.extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term=$$"
-        self.extra_settings["urlLabel"] = database + " Details:"
-        if useIframe:
-            self.extra_settings["iframeUrl"] = self.extra_settings["url"]
-            if not iframeHeight:
-                iframeHeight = "600"
-            if not iframeWidth:
-                iframeWidth = "800"
-            self.extra_settings["iframeOptions"] = "height= %s width= %s" % (iframeHeight, iframeWidth)
-
-    def getSeqType(self, inputFile):
-        with open(inputFile, "r") as bigpsl:
-            sampleSeq = bigpsl.readline().split()
-        if len(sampleSeq) == 25:
-            return sampleSeq[-1]
-        else:
-            return "-1"        
-    '''
\ No newline at end of file
diff -r 7486909dfc22 -r fa990284327b datatypes/Datatype.pyc
Binary file datatypes/Datatype.pyc has changed
diff -r 7486909dfc22 -r fa990284327b datatypes/binary/BigBed.py
--- a/datatypes/binary/BigBed.py	Fri Sep 29 14:50:50 2017 -0400
+++ b/datatypes/binary/BigBed.py	Mon Oct 30 11:58:31 2017 -0400
@@ -36,13 +36,12 @@
             self.database_settings = DatabaseIndex(database=self.trackSettings["database"], seqType=self.seqType).setExtLink()
             self.extraSettings.update(self.database_settings)
         if "indexIx" in self.trackSettings and "indexIxx" in self.trackSettings:
-            if not "trix_id" in self.trackSettings or not self.trackSettings["trix_id"]:
-                logging.error("Didn't specify the search index. To use TRIX index, you need to specify the identifiers")
-                exit(1)   
-            trix_id = self.trackSettings["trix_id"]
-            self.trix_settings = TrixIndex(indexIx=self.trackSettings["indexIx"], indexIxx=self.trackSettings["indexIxx"], trackName=self.trackName, mySpecieFolderPath=self.mySpecieFolderPath, trixId=trix_id).setExtLink()
+            self.trix_id = self.extraSettings["trix_id"]
+            if not self.trix_id:
+                logging.info("Didn't specify the ID for Trix index for BigBed file: %s. \n Will use \"name\" as default", self.trackName)
+            self.trix_settings = TrixIndex(indexIx=self.trackSettings["indexIx"], indexIxx=self.trackSettings["indexIxx"], trackName=self.trackName, mySpecieFolderPath=self.mySpecieFolderPath, trixId=self.trix_id).setExtLink()
             self.extraSettings.update(self.trix_settings)
-    
+
     def validateData(self):
         self.validator = DataValidation(self.inputFile, self.dataType, self.chromSizesFile.name)
         self.validator.validate()
diff -r 7486909dfc22 -r fa990284327b datatypes/binary/BigBed.pyc
Binary file datatypes/binary/BigBed.pyc has changed
diff -r 7486909dfc22 -r fa990284327b datatypes/interval/BigPsl.py
--- a/datatypes/interval/BigPsl.py	Fri Sep 29 14:50:50 2017 -0400
+++ b/datatypes/interval/BigPsl.py	Mon Oct 30 11:58:31 2017 -0400
@@ -3,7 +3,6 @@
 import os
 import tempfile
 import string
-import logging
 
 from Interval import Interval
 from util.index.DatabaseIndex import DatabaseIndex
@@ -35,18 +34,15 @@
             self.extraSettings["group"] = self.trackSettings["group_name"]
         self.extraSettings["visibility"] = "dense"
         self.extraSettings["priority"] = self.trackSettings["order_index"]
-        #self.extraSettings["searchIndex"] = "name"
+        self.extraSettings["searchIndex"] = "name"
         if self.seqType is None:
             self.seqType = self._getSeqType()
         if "database" in self.trackSettings:
             self.database_settings = DatabaseIndex(database=self.trackSettings["database"], seqType=self.seqType).setExtLink()
             self.extraSettings.update(self.database_settings)
         if "indexIx" in self.trackSettings and "indexIxx" in self.trackSettings:
-            if not "trix_id" in self.trackSettings or not self.trackSettings["trix_id"]:
-                logging.error("Didn't specify the search index. To use TRIX index, you need to specify the identifiers")
-                exit(1)   
             trix_id = self.trackSettings["trix_id"]
-            self.trix_settings = TrixIndex(indexIx=self.trackSettings["indexIx"], indexIxx=self.trackSettings["indexIxx"], trackName=self.trackName, mySpecieFolderPath=self.mySpecieFolderPath, trixId = trix_id, default_index = "name").setExtLink()
+            self.trix_settings = TrixIndex(indexIx=self.trackSettings["indexIx"], indexIxx=self.trackSettings["indexIxx"], trackName=self.trackName, mySpecieFolderPath=self.mySpecieFolderPath).setExtLink()
             self.extraSettings.update(self.trix_settings)
             
 
diff -r 7486909dfc22 -r fa990284327b datatypes/interval/BigPsl.pyc
Binary file datatypes/interval/BigPsl.pyc has changed
diff -r 7486909dfc22 -r fa990284327b hubArchiveCreator.xml
--- a/hubArchiveCreator.xml	Fri Sep 29 14:50:50 2017 -0400
+++ b/hubArchiveCreator.xml	Mon Oct 30 11:58:31 2017 -0400
@@ -123,15 +123,8 @@
                 #set database = str($f.formatChoice.bedChoice.database)
                 #silent $extra_data_dict.update({"database": $database})
                 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
-                    #set trix_id = str($f.formatChoice.bedChoice.add_trix_index.trix_id)
-                    #silent $extra_data_dict.update({"trix_id": $trix_id})
-                    #if $f.formatChoice.bedChoice.add_trix_index.index_files.index_files_type == "collection"
-                        #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.trix_index.index_ix)
-                        #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.trix_index.index_ixx)
-                    #else 
-                        #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.index_ix)
-                        #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.index_ixx)
-                    #end if
+                    #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ix)
+                    #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ixx)
                     #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
                 #end if
                 #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
@@ -141,15 +134,8 @@
                 #set database = str($f.formatChoice.bedChoice.database)
                 #silent $extra_data_dict.update({"database": $database})
                 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
-                    #set trix_id = str($f.formatChoice.bedChoice.add_trix_index.trix_id)
-                    #silent $extra_data_dict.update({"trix_id": $trix_id})
-                    #if $f.formatChoice.bedChoice.add_trix_index.index_files.index_files_type == "collection"
-                        #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.trix_index.index_ix)
-                        #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.trix_index.index_ixx)
-                    #else 
-                        #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.index_ix)
-                        #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.index_ixx)
-                    #end if
+                    #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ix)
+                    #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ixx)
                     #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
                 #end if
                 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
@@ -166,16 +152,10 @@
         #end if
         #if $f.formatChoice.format_select == "bigbed"
             #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes"
-                    #set trix_id = str($f.formatChoice.add_trix_index.trix_id)
-                    #silent $extra_data_dict.update({"trix_id": $trix_id})
-                    #if $f.formatChoice.add_trix_index.index_files.index_files_type == "collection"
-                        #set ix_index = str($f.formatChoice.add_trix_index.index_files.trix_index.index_ix)
-                        #set ixx_index = str($f.formatChoice.add_trix_index.index_files.trix_index.index_ixx)
-                    #else 
-                        #set ix_index = str($f.formatChoice.add_trix_index.index_files.index_ix)
-                        #set ixx_index = str($f.formatChoice.add_trix_index.index_files.index_ixx)
-                    #end if
-                    #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
+                #set ix_index = str($f.formatChoice.add_trix_index.add_trix_file.trix_index.index_ix)
+                #set ixx_index = str($f.formatChoice.add_trix_index.add_trix_file.trix_index.index_ixx)
+                #set trix_id = str($f.formatChoice.add_trix_index.add_trix_file.trix_id)
+                #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index, "trix_id": $trix_id})
             #end if
             #silent $prepare_json("BigBed", $f.formatChoice.BIGBED, $index_track_final,
                                             $extra_data_dict)
@@ -377,7 +357,13 @@
                                 label="BIGBED File"
                         />
                         <expand macro="add_trix_file">
-                            <expand macro="specify_search_index" />
+                            <param 
+                                name="trix_id" 
+                                value="name" 
+                                type="text"
+                                size="30"
+                                label="Specify Trix identifier"
+                            />
                         </expand>
                         <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
                         <param name="track_color" type="color" label="Track color" value="#000000">
diff -r 7486909dfc22 -r fa990284327b macros.xml
--- a/macros.xml	Fri Sep 29 14:50:50 2017 -0400
+++ b/macros.xml	Mon Oct 30 11:58:31 2017 -0400
@@ -52,50 +52,21 @@
 
     <xml name="add_trix_file">
         <conditional name="add_trix_index">
-            <param name="add_trix_index_selector" type="select" label="Add TRIX files that maps free text to a set of indices" >
+            <param name="add_trix_index_selector" type="select" label="Add Trix index that allow for fast look-up of free text associated with a list of identifiers." help="More about Trix index: https://genome.ucsc.edu/goldenpath/help/trix.html">
                 <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
 
             <when value="yes">
                 <param 
-                    name="trix_id" 
-                    value="name" 
-                    type="text"
-                    size="30"
-                    label="Specify Trix identifier"
-                    help="More about Trix index: https://genome.ucsc.edu/goldenpath/help/trix.html"
+                    name="trix_index" 
+                    format="txt" 
+                    type="data_collection" 
+                    collection_type="list" 
+                    label="Specify Trix index" 
+                    help="Dataset collection containing ix and ixx files generated by UCSC Trix Index Generator"
                 />
-                <conditional name="index_files">
-                    <param name="index_files_type" type="select" label="Single files or an index collection" help="Select between provide individual trix files (ix and ixx) or an trix index collection">
-                        <option value="collection">Index collection</option>
-                        <option value="single">Single files</option>
-                    </param>
-                    <when value="collection">
-                        <param 
-                            name="trix_index" 
-                            format="txt" 
-                            type="data_collection" 
-                            collection_type="list" 
-                            label="Select dataset collection" 
-                            help="Specify dataset collection containing ix and ixx files"
-                        />
-                    </when>
-                    <when value="single">
-                        <param
-                            format="txt"
-                            name="index_ix"
-                            type="data"
-                            label="Trix index file (ix)"
-                        />
-                        <param
-                            format="txt"
-                            name="index_ixx"
-                            type="data"
-                            label="Trix index file (ixx)"
-                        />
-                    </when>
-                </conditional>
+                <yield />
             </when>
             <when value="no">
             </when>
diff -r 7486909dfc22 -r fa990284327b util/index/ExternIndex.py
--- a/util/index/ExternIndex.py	Fri Sep 29 14:50:50 2017 -0400
+++ b/util/index/ExternIndex.py	Mon Oct 30 11:58:31 2017 -0400
@@ -13,48 +13,4 @@
     @abc.abstractmethod
     def setExtLink(self):
         """set external link"""
-        
-    
-    
-
-    '''
-    @staticmethod 
-    def setExtLink(database, inputFile, extra_settings, seqType=None, useIframe=True, iframeHeight=None, iframeWidth=None):
-        if "NCBI" in database:
-            if not seqType:
-                seqType = int(ExternIndex.getSeqType(inputFile))
-            else:
-                seqType = seqType
-            if seqType < 0:
-                print seqType
-                raise Exception("Sequence Type is not set for bigPsl. Stopping the application")
-            if seqType == 2:
-                extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/protein/$$"
-            elif seqType == 1:
-                extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/nuccore/$$"
-            else:
-                raise Exception("Sequence Type {0} is not valid for bigPsl. Stopping the application".format(seqType))
-        elif "UniProt" in database:
-            extra_settings["url"] = "http://www.uniprot.org/uniprot/$$"
-        elif "FlyBase" in database:
-            extra_settings["url"] = "http://flybase.org/reports/$$"
-        else:
-            extra_settings["url"] = "https://www.ncbi.nlm.nih.gov/gquery/?term=$$"
-        extra_settings["urlLabel"] = database + " Details:"
-        if useIframe:
-            extra_settings["iframeUrl"] = extra_settings["url"]
-            if not iframeHeight:
-                iframeHeight = "600"
-            if not iframeWidth:
-                iframeWidth = "800"
-            extra_settings["iframeOptions"] = "height= %s width= %s" % (iframeHeight, iframeWidth)
-
-    @staticmethod
-    def getSeqType(inputFile):
-        with open(inputFile, "r") as bigpsl:
-            sampleSeq = bigpsl.readline().split()
-        if len(sampleSeq) == 25:
-            return sampleSeq[-1]
-        else:
-            return "-1"        
-    '''
\ No newline at end of file
+        
\ No newline at end of file
diff -r 7486909dfc22 -r fa990284327b util/index/ExternIndex.pyc
Binary file util/index/ExternIndex.pyc has changed
diff -r 7486909dfc22 -r fa990284327b util/index/TrixIndex.py
--- a/util/index/TrixIndex.py	Fri Sep 29 14:50:50 2017 -0400
+++ b/util/index/TrixIndex.py	Mon Oct 30 11:58:31 2017 -0400
@@ -7,20 +7,19 @@
 from ExternIndex import ExternIndex
 
 class TrixIndex(ExternIndex):
-    def __init__(self, indexIx, indexIxx, trackName, mySpecieFolderPath, trixId, **args):
+    def __init__(self, indexIx, indexIxx, trackName, mySpecieFolderPath, **args):
+        self.logger = logging.getLogger(__name__)
         self.indexIx = indexIx
         self.indexIxx = indexIxx
         self.trackName = trackName
         self.mySpecieFolderPath = mySpecieFolderPath
-        self.trixId = trixId
         self.index_settings = collections.OrderedDict()
-        if "default_index" in args:
-            self.default_index = args["default_index"]
+        if "trixId" in args:
+            self.trixId = args["trixId"]
         else:
-            self.default_index = None
+            self.trixId = None
 
     def setExtLink(self):
-        self.setSearchIndex()
         self.moveIndexFile()
         self.index_settings["searchTrix"] = "trix/%s" % self.indexIxName
         return self.index_settings
@@ -39,13 +38,14 @@
         shutil.copyfile(self.indexIxx, self.indexIxxPath)
 
     def setSearchIndex(self):
-        if self.default_index:
+        if self.trixId:
             set_index = set()
             set_index.add(self.trixId)
-            set_index.add(self.default_index)
+            set_index.add("name")
             search_index = ",".join(set_index)
         else:
-            search_index = self.trixId
+            search_index = "name"
         logging.debug("trixId= %s, searchIndex= %s", self.trixId, search_index)
         self.index_settings["searchIndex"] = search_index
+    
         
diff -r 7486909dfc22 -r fa990284327b util/index/TrixIndex.pyc
Binary file util/index/TrixIndex.pyc has changed