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1 #!/usr/bin/python
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2 ## ********************************* Kipper *************************************
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3 ##
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4
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5 import vdb_common
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6 import vdb_data_stores
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7 import subprocess
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8 import json
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9 import glob
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10 import os
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11 import sys
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12
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13 class VDBKipperDataStore(vdb_data_stores.VDBDataStore):
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14
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15 metadata = None
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16 versions = None
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17 command = None
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18
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19 def __init__(self, retrieval_obj, spec_file_id):
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20 """
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21 Metadata (version list) is expected in "master/" subfolder of data_store_path on server.
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22
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23 Future: allow for more than one database / .md file in a folder?
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24 """
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25 super(VDBKipperDataStore, self).__init__(retrieval_obj, spec_file_id)
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26 # Ensure we're working with this tool's version of Kipper.
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27 self.command = os.path.join(os.path.dirname(sys._getframe().f_code.co_filename),'kipper.py')
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28 self.versions = []
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29
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30 metadata_path = os.path.join(self.data_store_path,'master','*.md')
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31 metadata_files = glob.glob(metadata_path)
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32
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33 if len(metadata_files) == 0:
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34 return # Handled by empty list error in versioned_data_form.py
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35
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36 metadata_file = metadata_files[0]
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37
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38 with open(metadata_file,'r') as metadata_handle:
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39 self.metadata = json.load(metadata_handle)
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40 for volume in self.metadata['volumes']:
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41 self.versions.extend(volume['versions'])
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42
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43 if len(self.versions) == 0:
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44 print "Error: Unable to locate metadata file: " + metadata_path
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45 sys.exit(1)
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46
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47 self.versions = sorted(self.versions, key=lambda x: x['id'], reverse=True)
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48
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49
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50 def get_version(self, version_name):
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51 """
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52 Trigger populating of the appropriate version folder.
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53 Returns path information to version folder, and its appropriate library label.
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54
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55 @param version_id string
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56 """
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57
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58 version = self.get_metadata_version(version_name)
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59
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60 if not version:
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61 print 'Error: Galaxy was not able to find the given version id in the %s data store.' % self.version_path
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62 sys.exit( 1 )
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63
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64 version_name = version['name']
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65 self.version_path = os.path.join(self.data_store_path, version_name)
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66 self.version_label = vdb_common.lightDate(version['created']) + '_v' + version_name
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67
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68 print self.library_label_path
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69 print self.version_label
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70
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71 self.library_version_path = os.path.join(self.library_label_path, self.version_label)
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72
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73 if not os.path.exists(self.version_path):
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74 try:
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75 os.mkdir(self.version_path)
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76 except:
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77 print 'Error: Galaxy was not able to create data store folder "%s". Check permissions?' % self.version_path
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78 sys.exit( 1 )
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79
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80 # Generate cache if folder is empty (can take a while):
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81 if os.listdir(self.version_path) == []:
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82
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83 db_file = os.path.join(self.data_store_path, 'master', self.metadata["db_file_name"] )
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84 command = [self.command, db_file, '-e','-I', version_name, '-o', self.version_path ]
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85
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86 try:
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87 result = subprocess.call(command);
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88 except:
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89 print 'Error: Galaxy was not able to run the kipper.py program successfully for this job: "%s". Check permissions?' % self.version_path
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90 sys.exit( 1 )
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91
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92
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93 def get_metadata_version(self, version_name=''):
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94 if version_name == '':
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95 return self.versions[0]
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96
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97 for version in self.versions:
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98 if str(version['name']) == version_name:
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99 return version
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100
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101 return False
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102
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