Mercurial > repos > shellac > guppy_basecaller
annotate env/bin/dynamodb_load @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
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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) |