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1 #!/usr/bin/python
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2 ## ********************************* GIT ARCHIVE *******************************
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3 ##
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4
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5 import os, sys
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6 import vdb_common
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7 import vdb_data_stores
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8 import subprocess
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9 import datetime
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10
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11 class VDBGitDataStore(vdb_data_stores.VDBDataStore):
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12
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13 def __init__(self, retrieval_obj, spec_file_id):
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14 """
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15 Archive is expected to be in "master/" subfolder of data_store_path on server.
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16 """
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17 super(VDBGitDataStore, self).__init__(retrieval_obj, spec_file_id)
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18 self.command = 'git'
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19 gitPath = self.data_store_path + 'master/'
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20 if not os.path.isdir(os.path.join(gitPath,'.git') ):
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21 print "Error: Unable to locate git archive file: " + gitPath
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22 sys.exit(1)
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23
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24 command = [self.command, '--git-dir=' + gitPath + '.git', '--work-tree=' + gitPath, 'for-each-ref','--sort=-*committerdate', "--format=%(*committerdate:raw) %(refname)"]
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25 # to list just 1 id: command.append('refs/tags/' + version_id)
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26 # git --git-dir=/.../NCBI_16S/master/.git --work-tree=/.../NCBI_16S/master/ tag
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27 items, error = subprocess.Popen(command,stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
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28 items = items.split("\n") #Loop through list of tags
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29 versions = []
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30 for ptr, item in enumerate(items):
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31
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32 # Ignore master branch name; time is included as separate field in all other cases
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33 if item.strip().find(" ") >0:
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34 (vtime, voffset, name) = item.split(" ")
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35 created = vdb_common.get_unix_time(vtime, voffset)
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36 item_name = name[10:] #strip 'refs/tags/' part off
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37 versions.append({'name':item_name, 'id':item_name, 'created': created})
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38
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39 self.versions = versions
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40
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41
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42 def get_version(self, version_name):
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43 """
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44 Returns server folder path to version folder containing git files for a given version_id (git tag)
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45
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46 FUTURE: TO AVOID USE CONFLICTS FOR VERSION RETRIEVAL, GIT CLONE INTO TEMP FOLDER
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47 with -s / --shared and -n / --no-checkout (to avoid head build) THEN CHECKOUT version
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48 ...
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49 REMOVE CLONE GIT REPO
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50
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51 @param galaxy_instance object A Bioblend galaxy instance
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52 @param library_id string Identifier for a galaxy data library
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53 @param library_label_path string Full hierarchic label of a library file or folder, PARENT of version id folder.
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54
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55 @param base_folder_id string a library folder id under which version files should exist
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56 @param version_id alphaneumeric string (git tag)
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57
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58 """
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59 version = self.get_metadata_version(version_name)
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60
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61 if not version:
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62 print 'Error: Galaxy was not able to find the given version id in the %s data store.' % self.version_path
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63 sys.exit( 1 )
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64
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65 version_name = version['name']
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66 self.version_path = os.path.join(self.data_store_path, version_name)
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67 self.version_label = vdb_common.lightDate(version['created']) + '_v' + version_name
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68 self.library_version_path = os.path.join(self.library_label_path, self.version_label)
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69
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70 # If Data Library Versioned Data folder doesn't exist for this version, then create it
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71 if not os.path.exists(self.version_path):
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72 try:
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73 os.mkdir(self.version_path)
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74 except:
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75 print 'Error: Galaxy was not able to create data store folder "%s". Check permissions?' % self.version_path
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76 sys.exit( 1 )
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77
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78 if os.listdir(self.version_path) == []:
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79
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80 git_path = self.data_store_path + 'master/'
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81 # RETRIEVE LIST OF FILES FOR GIVEN GIT TAG (using "ls-tree".
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82 # It can happen independently of git checkout)
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83
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84 command = [self.command, '--git-dir=%s/.git' % git_path, 'ls-tree','--name-only','-r', version_name]
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85 items, error = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
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86 git_files = items.split('\n')
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87
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88 # PERFORM GIT CHECKOUT
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89 command = [self.command, '--git-dir=%s/.git' % git_path, '--work-tree=%s' % git_path, 'checkout', version_name]
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90 results, error = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
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91
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92 vdb_common.move_files(git_path, self.version_path, git_files)
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93
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94
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95
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96 def get_metadata_version(self, version_name=''):
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97 if version_name == '':
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98 return self.versions[0]
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99
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100 for version in self.versions:
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101 if str(version['name']) == version_name:
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102 return version
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103
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104 return False
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105
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106
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