diff util/index/TrixIndex.py @ 83:0bc486356e2a draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/index/TrixIndex.py	Mon Oct 30 12:01:23 2017 -0400
@@ -0,0 +1,51 @@
+#!/usr/bin/python
+
+import os
+import collections
+import shutil
+import logging
+from ExternIndex import ExternIndex
+
+class TrixIndex(ExternIndex):
+    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.index_settings = collections.OrderedDict()
+        if "trixId" in args:
+            self.trixId = args["trixId"]
+        else:
+            self.trixId = None
+
+    def setExtLink(self):
+        self.moveIndexFile()
+        self.index_settings["searchTrix"] = "trix/%s" % self.indexIxName
+        return self.index_settings
+
+    def moveIndexFile(self):
+        indexFolder = os.path.join(self.mySpecieFolderPath, 'trix')
+        self.indexIxName = "".join( ( self.trackName, ".ix") )
+        self.indexIxxName = "".join( ( self.trackName, ".ixx") )
+        if not os.path.exists(indexFolder):
+            os.makedirs(indexFolder)
+        
+        # Move index files to the index folder
+        self.indexIxPath = os.path.join(indexFolder, self.indexIxName)
+        shutil.copyfile(self.indexIx, self.indexIxPath)
+        self.indexIxxPath = os.path.join(indexFolder, self.indexIxxName)
+        shutil.copyfile(self.indexIxx, self.indexIxxPath)
+
+    def setSearchIndex(self):
+        if self.trixId:
+            set_index = set()
+            set_index.add(self.trixId)
+            set_index.add("name")
+            search_index = ",".join(set_index)
+        else:
+            search_index = "name"
+        logging.debug("trixId= %s, searchIndex= %s", self.trixId, search_index)
+        self.index_settings["searchIndex"] = search_index
+    
+