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

Uploaded correct file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_stores/vdb_kipper.py	Sun Aug 09 16:07:50 2015 -0400
@@ -0,0 +1,102 @@
+#!/usr/bin/python
+## ********************************* Kipper *************************************
+##
+
+import vdb_common
+import vdb_data_stores
+import subprocess
+import json
+import glob
+import os
+import sys
+
+class VDBKipperDataStore(vdb_data_stores.VDBDataStore):
+	
+	metadata = None
+	versions = None
+	command = None
+	
+	def __init__(self, retrieval_obj, spec_file_id):
+		"""
+		Metadata (version list) is expected in "master/" subfolder of data_store_path on server. 
+		
+		Future: allow for more than one database / .md file in a folder?
+		"""
+		super(VDBKipperDataStore, self).__init__(retrieval_obj, spec_file_id)
+		# Ensure we're working with this tool's version of Kipper.
+		self.command = os.path.join(os.path.dirname(sys._getframe().f_code.co_filename),'kipper.py')
+		self.versions = []
+			
+		metadata_path = os.path.join(self.data_store_path,'master','*.md')
+		metadata_files = glob.glob(metadata_path)
+
+		if len(metadata_files) == 0:
+			return			# Handled by empty list error in versioned_data_form.py
+		
+		metadata_file = metadata_files[0]
+
+		with open(metadata_file,'r') as metadata_handle:
+			self.metadata = json.load(metadata_handle)
+			for volume in self.metadata['volumes']:
+				self.versions.extend(volume['versions']) 						
+	
+		if len(self.versions) == 0:
+			print "Error: Unable to locate metadata file: " + metadata_path
+			sys.exit(1) 
+		
+		self.versions = sorted(self.versions, key=lambda x: x['id'], reverse=True)
+				
+			
+	def get_version(self, version_name):
+		"""
+		Trigger populating of the appropriate version folder.  
+		Returns path information to version folder, and its appropriate library label. 
+		
+		@param version_id string
+		"""
+
+		version = self.get_metadata_version(version_name)
+
+		if not version:
+			print 'Error: Galaxy was not able to find the given version id in the %s data store.' % self.version_path
+			sys.exit( 1 )
+		
+		version_name = version['name']
+		self.version_path = os.path.join(self.data_store_path, version_name)
+		self.version_label = vdb_common.lightDate(version['created']) + '_v' + version_name
+		
+		print self.library_label_path
+		print self.version_label
+
+		self.library_version_path = os.path.join(self.library_label_path, self.version_label)
+
+		if not os.path.exists(self.version_path):
+			try:		
+				os.mkdir(self.version_path)
+			except:
+				print 'Error: Galaxy was not able to create data store folder "%s".  Check permissions?' % self.version_path
+				sys.exit( 1 )
+
+		# Generate cache if folder is empty (can take a while):
+		if os.listdir(self.version_path) == []: 
+
+			db_file = os.path.join(self.data_store_path, 'master', self.metadata["db_file_name"] )
+			command = [self.command, db_file, '-e','-I', version_name, '-o', self.version_path ]
+
+			try:
+				result = subprocess.call(command);
+			except:
+				print 'Error: Galaxy was not able to run the kipper.py program successfully for this job: "%s".  Check permissions?' % self.version_path
+				sys.exit( 1 )
+		
+
+	def get_metadata_version(self, version_name=''):
+		if version_name == '':
+			return self.versions[0]
+
+		for version in self.versions:
+			if str(version['name']) == version_name:
+				return version
+							
+		return False
+