Mercurial > repos > shellac > guppy_basecaller

annotate env/bin/dynamodb_dump @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 #!/Users/pldms/Development/Projects/2020/david-matthews-galaxy/guppy_basecaller/env/bin/python3
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2
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3 import argparse
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4 import errno
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5 import os
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6
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7 import boto
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8 from boto.compat import json
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9 from boto.compat import six
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10
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11
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12 DESCRIPTION = """Dump the contents of one or more DynamoDB tables to the local filesystem.
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13
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14 Each table is dumped into two files:
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15 - {table_name}.metadata stores the table's name, schema and provisioned
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16 throughput.
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17 - {table_name}.data stores the table's actual contents.
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18
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19 Both files are created in the current directory. To write them somewhere else,
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20 use the --out-dir parameter (the target directory will be created if needed).
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21 """
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22
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23
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24 def dump_table(table, out_dir):
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25 metadata_file = os.path.join(out_dir, "%s.metadata" % table.name)
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26 data_file = os.path.join(out_dir, "%s.data" % table.name)
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27
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28 with open(metadata_file, "w") as metadata_fd:
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29 json.dump(
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30 {
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31 "name": table.name,
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32 "schema": table.schema.dict,
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33 "read_units": table.read_units,
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34 "write_units": table.write_units,
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35 },
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36 metadata_fd
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37 )
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38
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39 with open(data_file, "w") as data_fd:
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40 for item in table.scan():
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41 # JSON can't serialize sets -- convert those to lists.
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42 data = {}
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43 for k, v in six.iteritems(item):
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44 if isinstance(v, (set, frozenset)):
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45 data[k] = list(v)
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46 else:
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47 data[k] = v
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48
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49 data_fd.write(json.dumps(data))
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50 data_fd.write("\n")
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51
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52
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53 def dynamodb_dump(tables, out_dir):
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54 try:
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55 os.makedirs(out_dir)
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56 except OSError as e:
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57 # We don't care if the dir already exists.
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58 if e.errno != errno.EEXIST:
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59 raise
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60
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61 conn = boto.connect_dynamodb()
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62 for t in tables:
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63 dump_table(conn.get_table(t), out_dir)
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64
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65
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66 if __name__ == "__main__":
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67 parser = argparse.ArgumentParser(
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68 prog="dynamodb_dump",
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69 description=DESCRIPTION
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70 )
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71 parser.add_argument("--out-dir", default=".")
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72 parser.add_argument("tables", metavar="TABLES", nargs="+")
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73
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74 namespace = parser.parse_args()
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75
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76 dynamodb_dump(namespace.tables, namespace.out_dir)