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| 1 | +# August 6, 2018 |
| 2 | +# Create parameters for the ssh/scp remote file upload commands |
| 3 | + |
| 4 | + |
| 5 | +from json import loads, dumps |
| 6 | + |
| 7 | +from qiita_db.sql_connection import TRN |
| 8 | +from qiita_db.software import Software, Command |
| 9 | +from qiita_db.exceptions import (QiitaDBError, QiitaDBDuplicateError) |
| 10 | +from qiita_db.util import convert_to_id |
| 11 | + |
| 12 | + |
| 13 | +# Copied from patch 58.py. Couldn't import due to how patching system works |
| 14 | +def create_command(software, name, description, parameters, outputs=None, |
| 15 | + analysis_only=False): |
| 16 | + r"""Replicates the Command.create code at the time the patch was written""" |
| 17 | + # Perform some sanity checks in the parameters dictionary |
| 18 | + if not parameters: |
| 19 | + raise QiitaDBError( |
| 20 | + "Error creating command %s. At least one parameter should " |
| 21 | + "be provided." % name) |
| 22 | + sql_param_values = [] |
| 23 | + sql_artifact_params = [] |
| 24 | + for pname, vals in parameters.items(): |
| 25 | + if len(vals) != 2: |
| 26 | + raise QiitaDBError( |
| 27 | + "Malformed parameters dictionary, the format should be " |
| 28 | + "{param_name: [parameter_type, default]}. Found: " |
| 29 | + "%s for parameter name %s" % (vals, pname)) |
| 30 | + |
| 31 | + ptype, dflt = vals |
| 32 | + # Check that the type is one of the supported types |
| 33 | + supported_types = ['string', 'integer', 'float', 'reference', |
| 34 | + 'boolean', 'prep_template', 'analysis'] |
| 35 | + if ptype not in supported_types and not ptype.startswith( |
| 36 | + ('choice', 'mchoice', 'artifact')): |
| 37 | + supported_types.extend(['choice', 'mchoice', 'artifact']) |
| 38 | + raise QiitaDBError( |
| 39 | + "Unsupported parameters type '%s' for parameter %s. " |
| 40 | + "Supported types are: %s" |
| 41 | + % (ptype, pname, ', '.join(supported_types))) |
| 42 | + |
| 43 | + if ptype.startswith(('choice', 'mchoice')) and dflt is not None: |
| 44 | + choices = set(loads(ptype.split(':')[1])) |
| 45 | + dflt_val = dflt |
| 46 | + if ptype.startswith('choice'): |
| 47 | + # In the choice case, the dflt value is a single string, |
| 48 | + # create a list with it the string on it to use the |
| 49 | + # issuperset call below |
| 50 | + dflt_val = [dflt_val] |
| 51 | + else: |
| 52 | + # jsonize the list to store it in the DB |
| 53 | + dflt = dumps(dflt) |
| 54 | + if not choices.issuperset(dflt_val): |
| 55 | + raise QiitaDBError( |
| 56 | + "The default value '%s' for the parameter %s is not " |
| 57 | + "listed in the available choices: %s" |
| 58 | + % (dflt, pname, ', '.join(choices))) |
| 59 | + |
| 60 | + if ptype.startswith('artifact'): |
| 61 | + atypes = loads(ptype.split(':')[1]) |
| 62 | + sql_artifact_params.append( |
| 63 | + [pname, 'artifact', atypes]) |
| 64 | + else: |
| 65 | + if dflt is not None: |
| 66 | + sql_param_values.append([pname, ptype, False, dflt]) |
| 67 | + else: |
| 68 | + sql_param_values.append([pname, ptype, True, None]) |
| 69 | + |
| 70 | + with TRN: |
| 71 | + sql = """SELECT EXISTS(SELECT * |
| 72 | + FROM qiita.software_command |
| 73 | + WHERE software_id = %s AND name = %s)""" |
| 74 | + TRN.add(sql, [software.id, name]) |
| 75 | + if TRN.execute_fetchlast(): |
| 76 | + raise QiitaDBDuplicateError( |
| 77 | + "command", "software: %d, name: %s" |
| 78 | + % (software.id, name)) |
| 79 | + # Add the command to the DB |
| 80 | + sql = """INSERT INTO qiita.software_command |
| 81 | + (name, software_id, description, is_analysis) |
| 82 | + VALUES (%s, %s, %s, %s) |
| 83 | + RETURNING command_id""" |
| 84 | + sql_params = [name, software.id, description, analysis_only] |
| 85 | + TRN.add(sql, sql_params) |
| 86 | + c_id = TRN.execute_fetchlast() |
| 87 | + |
| 88 | + # Add the parameters to the DB |
| 89 | + sql = """INSERT INTO qiita.command_parameter |
| 90 | + (command_id, parameter_name, parameter_type, required, |
| 91 | + default_value) |
| 92 | + VALUES (%s, %s, %s, %s, %s) |
| 93 | + RETURNING command_parameter_id""" |
| 94 | + sql_params = [[c_id, pname, p_type, reqd, default] |
| 95 | + for pname, p_type, reqd, default in sql_param_values] |
| 96 | + TRN.add(sql, sql_params, many=True) |
| 97 | + TRN.execute() |
| 98 | + |
| 99 | + # Add the artifact parameters |
| 100 | + sql_type = """INSERT INTO qiita.parameter_artifact_type |
| 101 | + (command_parameter_id, artifact_type_id) |
| 102 | + VALUES (%s, %s)""" |
| 103 | + supported_types = [] |
| 104 | + for pname, p_type, atypes in sql_artifact_params: |
| 105 | + sql_params = [c_id, pname, p_type, True, None] |
| 106 | + TRN.add(sql, sql_params) |
| 107 | + pid = TRN.execute_fetchlast() |
| 108 | + sql_params = [[pid, convert_to_id(at, 'artifact_type')] |
| 109 | + for at in atypes] |
| 110 | + TRN.add(sql_type, sql_params, many=True) |
| 111 | + supported_types.extend([atid for _, atid in sql_params]) |
| 112 | + |
| 113 | + # If the software type is 'artifact definition', there are a couple |
| 114 | + # of extra steps |
| 115 | + if software.type == 'artifact definition': |
| 116 | + # If supported types is not empty, link the software with these |
| 117 | + # types |
| 118 | + if supported_types: |
| 119 | + sql = """INSERT INTO qiita.software_artifact_type |
| 120 | + (software_id, artifact_type_id) |
| 121 | + VALUES (%s, %s)""" |
| 122 | + sql_params = [[software.id, atid] |
| 123 | + for atid in supported_types] |
| 124 | + TRN.add(sql, sql_params, many=True) |
| 125 | + # If this is the validate command, we need to add the |
| 126 | + # provenance and name parameters. These are used internally, |
| 127 | + # that's why we are adding them here |
| 128 | + if name == 'Validate': |
| 129 | + sql = """INSERT INTO qiita.command_parameter |
| 130 | + (command_id, parameter_name, parameter_type, |
| 131 | + required, default_value) |
| 132 | + VALUES (%s, 'name', 'string', 'False', |
| 133 | + 'dflt_name'), |
| 134 | + (%s, 'provenance', 'string', 'False', NULL) |
| 135 | + """ |
| 136 | + TRN.add(sql, [c_id, c_id]) |
| 137 | + |
| 138 | + # Add the outputs to the command |
| 139 | + if outputs: |
| 140 | + sql = """INSERT INTO qiita.command_output |
| 141 | + (name, command_id, artifact_type_id) |
| 142 | + VALUES (%s, %s, %s)""" |
| 143 | + sql_args = [[pname, c_id, convert_to_id(at, 'artifact_type')] |
| 144 | + for pname, at in outputs.items()] |
| 145 | + TRN.add(sql, sql_args, many=True) |
| 146 | + TRN.execute() |
| 147 | + |
| 148 | + return Command(c_id) |
| 149 | + |
| 150 | + |
| 151 | +with TRN: |
| 152 | + qiita_plugin = Software.from_name_and_version('Qiita', 'alpha') |
| 153 | + |
| 154 | + # Create the 'list_remote_files' command |
| 155 | + parameters = {'url': ['string', None], |
| 156 | + 'private_key': ['string', None]} |
| 157 | + create_command(qiita_plugin, "list_remote_files", |
| 158 | + "retrieves list of valid study files from remote dir", |
| 159 | + parameters) |
| 160 | + |
| 161 | + # Create the 'download_remote_files' command |
| 162 | + parameters = {'url': ['string', None], |
| 163 | + 'destination': ['string', None], |
| 164 | + 'private_key': ['string', None]} |
| 165 | + create_command(qiita_plugin, "download_remote_files", |
| 166 | + "downloads valid study files from remote dir", parameters) |
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