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

Uploaded correct file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_stores/vdb_git.py	Sun Aug 09 16:07:50 2015 -0400
@@ -0,0 +1,106 @@
+#!/usr/bin/python
+## ********************************* GIT ARCHIVE *******************************
+##
+
+import os, sys
+import vdb_common
+import vdb_data_stores
+import subprocess
+import datetime
+
+class VDBGitDataStore(vdb_data_stores.VDBDataStore):
+
+	def __init__(self, retrieval_obj, spec_file_id):
+		"""
+		Archive is expected to be in "master/" subfolder of data_store_path on server.  
+		"""
+		super(VDBGitDataStore, self).__init__(retrieval_obj, spec_file_id)
+		self.command = 'git'
+		gitPath = self.data_store_path + 'master/'
+		if not os.path.isdir(os.path.join(gitPath,'.git') ):
+			print "Error: Unable to locate git archive file: " + gitPath
+			sys.exit(1) 
+		
+		command = [self.command, '--git-dir=' + gitPath + '.git', '--work-tree=' + gitPath, 'for-each-ref','--sort=-*committerdate', "--format=%(*committerdate:raw) %(refname)"]
+		#	to list just 1 id: command.append('refs/tags/' + version_id)
+		# git --git-dir=/.../NCBI_16S/master/.git --work-tree=/.../NCBI_16S/master/ tag
+		items, error = subprocess.Popen(command,stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
+		items = items.split("\n") #Loop through list of tags
+		versions = []
+		for ptr, item in enumerate(items):
+
+			# Ignore master branch name; time is included as separate field in all other cases
+			if item.strip().find(" ") >0: 
+				(vtime, voffset, name) = item.split(" ")
+				created = vdb_common.get_unix_time(vtime, voffset)
+				item_name = name[10:] #strip 'refs/tags/' part off
+				versions.append({'name':item_name, 'id':item_name, 'created': created})
+		
+		self.versions = versions
+
+	
+	def get_version(self, version_name):
+		"""
+		Returns server folder path to version folder containing git files for a given version_id (git tag)
+		
+		FUTURE: TO AVOID USE CONFLICTS FOR VERSION RETRIEVAL, GIT CLONE INTO TEMP FOLDER 
+		with -s / --shared and -n / --no-checkout (to avoid head build) THEN CHECKOUT version
+		...
+		REMOVE CLONE GIT REPO
+
+		@param galaxy_instance object A Bioblend galaxy instance
+		@param library_id string Identifier for a galaxy data library
+		@param library_label_path string Full hierarchic label of a library file or folder, PARENT of version id folder.
+
+		@param base_folder_id string a library folder id under which version files should exist	
+		@param version_id alphaneumeric string (git tag)
+		
+		"""
+		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
+		self.library_version_path = os.path.join(self.library_label_path, self.version_label)
+
+		# If Data Library Versioned Data folder doesn't exist for this version, then create it
+		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 )
+
+		if os.listdir(self.version_path) == []: 	
+			
+			git_path = self.data_store_path + 'master/'
+			# RETRIEVE LIST OF FILES FOR GIVEN GIT TAG (using "ls-tree".  
+			# It can happen independently of git checkout)
+
+			command = [self.command,  '--git-dir=%s/.git' % git_path, 'ls-tree','--name-only','-r', version_name]
+			items, error = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
+			git_files = items.split('\n')
+		
+			# PERFORM GIT CHECKOUT 
+			command = [self.command, '--git-dir=%s/.git' % git_path, '--work-tree=%s' % git_path, 'checkout', version_name]
+			results, error = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()		
+		
+			vdb_common.move_files(git_path, self.version_path, git_files)
+
+
+
+	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
+		
+