diff data_stores/vdb_folder.py @ 1:5c5027485f7d draft

Uploaded correct file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_stores/vdb_folder.py	Sun Aug 09 16:07:50 2015 -0400
@@ -0,0 +1,90 @@
+#!/usr/bin/python
+## ******************************* FILE FOLDER *********************************
+##
+
+import re
+import os
+import vdb_common
+import vdb_data_stores
+
+class VDBFolderDataStore(vdb_data_stores.VDBDataStore):
+
+	versions = None
+	library = None
+	
+	def __init__(self, retrieval_obj, spec_file_id):
+		"""
+		Provides list of available versions where each version is indicated by the 
+		existence of a folder that contains its content.  This content can be directly
+		in the galaxy Versioned Data folder tree, OR it can be linked to another folder
+		on the server.  In the latter case, galaxy will treat the Versioned Data folders as caches.
+		View of versions filters out any folders that are used for derivative data caching.
+		"""
+		super(VDBFolderDataStore, self).__init__(retrieval_obj, spec_file_id)
+
+		self.library = retrieval_obj.library
+		
+		versions = []
+		
+		# If data source spec file has no content, use the library folder directly.
+		# Name of EACH subfolder should be a label for each version, including date/time and version id.
+		if self.data_store_path == '':
+			try:
+				lib_label_len = len(self.library_label_path) +1 
+			
+				for item in self.library:
+					# If item is under library_label_path ...
+					if item['name'][0:lib_label_len] == self.library_label_path + '/':
+						item_name = item['name'][lib_label_len:len(item['name'])]
+						if item_name.find('/') == -1 and item_name.find('_') != -1:
+							(item_date, item_version) = item_name.split('_',1)
+							created = vdb_common.parse_date(item_date)	
+							versions.append({'name':item_name, 'id':item_name, 'created': created})
+		
+			except Exception as err: 
+				# This is the first call to api so api url or authentication erro can happen here.
+				versions.append({
+					'name':'Software Error: Unable to get version list: ' + err.message, 
+					'id':'',
+					'created':''
+				})
+
+		else:
+
+			base_file_path = self.data_store_path
+			#base_file_path = os.path.dirname(self.base_file_name)
+			#Here we need to get directory listing of linked file location.
+			for item_name in os.listdir(base_file_path): # Includes files and folders
+				# Only interested in folders
+				if os.path.isdir( os.path.join(base_file_path, item_name)) and  item_name.find('_') != -1:
+					(item_date, item_version) = item_name.split('_',1)
+					created = vdb_common.parse_date(item_date)	
+					versions.append({'name':item_name, 'id':item_name, 'created': created})
+
+		
+		self.versions = sorted(versions, key=lambda x: x['name'], reverse=True)
+				
+	def get_version(self, version_name):
+		"""
+		Return server path of requested version info - BUT ONLY IF IT IS LINKED.
+		IF NOT LINKED, returns None for self.version_path
+		
+		QUESTION: DOES GALAXY AUTOMATICALLY HANDLE tar.gz/zip decompression?
+		
+		@uses library_label_path string Full hierarchic label of a library file or folder, PARENT of version id folder.
+		@uses base_file_name string Server absolute path to data_store spec file
+
+		@param version_name alphaneumeric string (git tag)
+		"""
+		self.version_label = version_name
+		self.library_version_path = os.path.join(self.library_label_path, self.version_label)
+
+		if self.data_store_path == '':
+			# In this case version content is held in library directly; 
+			self.version_path = self.base_file_name
+
+		else:
+
+			#linked to some other folder, spec is location of base_file_name
+			self.version_path = os.path.join(self.data_store_path, version_name)
+