diff util/index/TrixIndex.py @ 29:7e8a8b732db3 draft

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
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util/index/TrixIndex.py	Wed May 16 18:04:20 2018 -0400
@@ -0,0 +1,45 @@
+#!/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, trixId, **args):
+        self.logger = logging.getLogger(__name__)
+        self.indexIx = indexIx
+        self.indexIxx = indexIxx
+        self.trackName = trackName
+        self.mySpecieFolderPath = mySpecieFolderPath
+        self.index_settings = collections.OrderedDict()
+        self.trixId = trixId.rstrip()
+        
+
+    def setExtLink(self):
+        self.setSearchIndex()
+        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 not self.trixId:
+            self.logger.error("Didn't specify Trix Id")
+        self.logger.debug("trixId= %s, searchIndex= %s", self.trixId, self.trixId)
+        self.index_settings["searchIndex"] = self.trixId
+    
+