Mercurial > repos > shellac > guppy_basecaller

annotate env/bin/dynamodb_load @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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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 os
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5
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6 import boto
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7 from boto.compat import json
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8 from boto.compat import six
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9 from boto.dynamodb.schema import Schema
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10
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11
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12 DESCRIPTION = """Load data into one or more DynamoDB tables.
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13
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14 For each table, data is read from two files:
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15 - {table_name}.metadata for the table's name, schema and provisioned
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16 throughput (only required if creating the table).
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17 - {table_name}.data for the table's actual contents.
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18
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19 Both files are searched for in the current directory. To read them from
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20 somewhere else, use the --in-dir parameter.
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21
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22 This program does not wipe the tables prior to loading data. However, any
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23 items present in the data files will overwrite the table's contents.
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24 """
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25
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26
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27 def _json_iterload(fd):
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28 """Lazily load newline-separated JSON objects from a file-like object."""
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29 buffer = ""
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30 eof = False
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31 while not eof:
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32 try:
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33 # Add a line to the buffer
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34 buffer += fd.next()
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35 except StopIteration:
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36 # We can't let that exception bubble up, otherwise the last
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37 # object in the file will never be decoded.
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38 eof = True
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39 try:
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40 # Try to decode a JSON object.
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41 json_object = json.loads(buffer.strip())
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42
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43 # Success: clear the buffer (everything was decoded).
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44 buffer = ""
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45 except ValueError:
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46 if eof and buffer.strip():
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47 # No more lines to load and the buffer contains something other
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48 # than whitespace: the file is, in fact, malformed.
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49 raise
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50 # We couldn't decode a complete JSON object: load more lines.
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51 continue
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52
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53 yield json_object
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54
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55
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56 def create_table(metadata_fd):
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57 """Create a table from a metadata file-like object."""
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58
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59
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60 def load_table(table, in_fd):
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61 """Load items into a table from a file-like object."""
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62 for i in _json_iterload(in_fd):
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63 # Convert lists back to sets.
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64 data = {}
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65 for k, v in six.iteritems(i):
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66 if isinstance(v, list):
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67 data[k] = set(v)
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68 else:
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69 data[k] = v
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70 table.new_item(attrs=data).put()
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71
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72
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73 def dynamodb_load(tables, in_dir, create_tables):
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74 conn = boto.connect_dynamodb()
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75 for t in tables:
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76 metadata_file = os.path.join(in_dir, "%s.metadata" % t)
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77 data_file = os.path.join(in_dir, "%s.data" % t)
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78 if create_tables:
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79 with open(metadata_file) as meta_fd:
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80 metadata = json.load(meta_fd)
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81 table = conn.create_table(
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82 name=t,
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83 schema=Schema(metadata["schema"]),
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84 read_units=metadata["read_units"],
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85 write_units=metadata["write_units"],
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86 )
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87 table.refresh(wait_for_active=True)
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88 else:
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89 table = conn.get_table(t)
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90
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91 with open(data_file) as in_fd:
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92 load_table(table, in_fd)
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93
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94
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95 if __name__ == "__main__":
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96 parser = argparse.ArgumentParser(
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97 prog="dynamodb_load",
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98 description=DESCRIPTION
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99 )
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100 parser.add_argument(
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101 "--create-tables",
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102 action="store_true",
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103 help="Create the tables if they don't exist already (without this flag, attempts to load data into non-existing tables fail)."
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104 )
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105 parser.add_argument("--in-dir", default=".")
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106 parser.add_argument("tables", metavar="TABLES", nargs="+")
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107
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108 namespace = parser.parse_args()
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109
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110 dynamodb_load(namespace.tables, namespace.in_dir, namespace.create_tables)