Mercurial > repos > iuc > data_manager_gemini_database_downloader

annotate data_manager/data_manager_gemini_download.py @ 4:fe5a9a7d95b0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:40:15 -0500
parents 172815da3d41
children b4b2b284230a
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1 #!/usr/bin/env python
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2
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172815da3d41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
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3 import datetime
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4 import json
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172815da3d41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
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5 import os
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6 import subprocess
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7 import sys
172815da3d41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
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fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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9 import yaml
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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12 def main():
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13 today = datetime.date.today()
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14 params = json.loads( open( sys.argv[1] ).read() )
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15 target_directory = params[ 'output_data' ][0]['extra_files_path']
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16 os.mkdir( target_directory )
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fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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17 # The target_directory needs to be specified twice for the following
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
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18 # invocation of gemini.
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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19 # In essence, the GEMINI_CONFIG environment variable makes gemini store
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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20 # its yaml configuration file in that directory, while the
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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21 # --annotation-dir argument makes it write the same path into the yaml
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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22 # file, which is then used for determining where the actual annotation
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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23 # files should be stored.
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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24 gemini_env = os.environ.copy()
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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25 gemini_env['GEMINI_CONFIG'] = target_directory
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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26 cmd = "gemini --annotation-dir %s update --dataonly %s %s" % (
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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27 target_directory,
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28 params['param_dict']['gerp_bp'],
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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29 params['param_dict']['cadd']
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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30 )
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31 subprocess.check_call( cmd, shell=True, env=gemini_env )
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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33 # modify the newly created gemini config file to contain a relative
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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34 # annotation dir path, which will be interpreted as relative to
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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35 # the job working directory at runtime by any gemini tool
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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36 config_file = os.path.join(target_directory, 'gemini-config.yaml')
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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37 with open(config_file) as fi:
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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38 config = yaml.load(fi)
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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39 config['annotation_dir'] = 'gemini/data'
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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40 with open(config_file, 'w') as fo:
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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41 yaml.dump(config, fo, allow_unicode=False, default_flow_style=False)
fe5a9a7d95b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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42
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43 data_manager_dict = {
3
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44 'data_tables': {
4
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45 'gemini_versioned_databases': [
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46 {
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47 'value': today.isoformat(),
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48 'dbkey': 'hg19',
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49 'version': params['param_dict']['gemini_db_version'],
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50 'name':
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51 'GEMINI annotations (%s snapshot)' % today.isoformat(),
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52 'path': './%s' % today.isoformat()
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53 }
3
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54 ]
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55 }
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56 }
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58 # save info to json file
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59 with open( sys.argv[1], 'wb' ) as out:
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60 out.write( json.dumps( data_manager_dict ) )
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61
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63 if __name__ == "__main__":
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64 main()