Mercurial > repos > ufz > lm_get_projects

annotate get_projects.py @ 0:a8eee1c3b6d7 draft default tip

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planemo upload for repository https://github.com/jw44lavo/galaxy-tools/blob/bgo/tools/lambdaminer/ commit 3f45cd07445498cefa73931cadf3d1115245ca1e
author ufz
date Mon, 17 Mar 2025 20:34:56 +0000
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a8eee1c3b6d7 planemo upload for repository https://github.com/jw44lavo/galaxy-tools/blob/bgo/tools/lambdaminer/ commit 3f45cd07445498cefa73931cadf3d1115245ca1e
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1 import argparse
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2 import os
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3 from json import load
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4
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6 import pandas as pd
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7 import sqlalchemy as db
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8
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9
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10 def get_arguments() -> argparse.Namespace:
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11 """
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12 Parse and return the command-line arguments required for the script.
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13
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14 return: argparse.Namespace: Parsed arguments containing credentials_file (str) and login (str).
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15 """
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16
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17 parser = argparse.ArgumentParser(
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18 description="Read the projects of the current user from the Lambda-Miner Database"
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19 )
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20
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21 # Add argument for the credentials file
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22 parser.add_argument(
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23 "-c",
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24 "--credentials-file",
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25 dest="credentials_file",
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26 type=str,
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27 required=False, # Optional
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28 help=(
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29 "Credential file in JSON format including dialect, user, password, host, port, and "
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30 "database. If not provided, the environment variable LAMBDAMINER_CREDENTIALS will be "
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31 "used."
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32 )
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33 )
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34
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35 # Add argument for the login name
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36 parser.add_argument(
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37 "-l",
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38 "--login-name",
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39 dest="login",
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40 type=str,
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41 required=True,
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42 help="UFZ login name of the user"
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43 )
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44
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45 # Add argument for the output file
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46 parser.add_argument(
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47 "-o",
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48 "--output-file",
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49 dest="output",
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50 type=str,
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51 default="projects.csv",
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52 help="Specifiy the output file path including the file name (default: 'projects.csv')"
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53 )
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54
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55 # Add argument for the type
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56 parser.add_argument(
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57 "-t",
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58 "--type",
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59 choices=["generic", "import", "calibration", "assignment", "validation", "export"],
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60 default="generic",
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61 help="Specify the workflow type (default: 'generic')"
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62 )
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63
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64 return parser.parse_args()
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65
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66
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67 def parse_check_args(args):
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68 """
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69 Parse and validate command line arguments.
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70
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71 Following actions are performed:
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72 - Check of the existence of the specified directory in the output path.
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73 - Assignment the correct credentials file to the arguments.
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74
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75 :param args: command line arguments.
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76 :type args: argparse.Namespace
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77 :raises FileNotFoundError: If the specified directory in the output path does not exist.
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78 """
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79
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80 # Extract the directory part of the specified output path
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81 dir_path = os.path.dirname(args.output) or "."
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82
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83 # Check if the directory exists and raise error if not
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84 if not os.path.isdir(dir_path):
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85 raise FileNotFoundError(f"Error: The directory does not exist: {dir_path}")
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86
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87 # Get environment variable LAMBDAMINER_CREDENTIALS
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88 envar_credentials = os.getenv("LAMBDAMINER_CREDENTIALS")
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89
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90 # Use the provided argument or fallback to the environment variable
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91 args.credentials_file = args.credentials_file or envar_credentials
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92
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93 assert args.credentials_file is not None, "Error: No credentials specified"
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94
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95
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96 def get_engine(credentials_path: str, echo: bool = False) -> db.engine.Engine:
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97 """
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98 Create and return a SQLAlchemy engine based on the supplied credentials.
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99
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100 The engine is created using the data from the supplied credentials file,
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101 which should be in JSON format and include the following keys:
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102 dialect, user, password, host, port, database
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103
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104 :param credentials_path: The path to the credentials file.
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105 :type credentials_path: str
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106 :return: The SQLAlchemy engine object.
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107 :rtype: sqlalchemy.engine.Engine
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108 """
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109
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110 with open(credentials_path) as file:
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111 credentials = load(file)
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112
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113 dialect = credentials["dialect"]
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114 username = credentials["user"]
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115 password = credentials["password"]
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116 host = credentials["host"]
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117 port = credentials["port"]
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118 database_name = credentials["database"]
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119
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120 database_url = f"{dialect}://{username}:{password}@{host}:{port}/{database_name}"
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121
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122 return db.create_engine(database_url, echo=echo)
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123
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124
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125 def get_user_id(connection, metadata, login: str) -> int:
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126 """
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127 Retrieve the user_id for a given login.
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128
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129 :param connection: The database connection.
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130 :param metadata: The database metadata containing table definitions.
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131 :param login: The login username to search for.
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132 :return: The user_id if found, otherwise None.
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133 """
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134
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135 # Access the 'ufz_user' table from metadata.
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136 User = metadata.tables["ufz_user"]
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137
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138 # Construct a query to select the user_id where the login matches.
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139 query = db.select(User.c.user_id).where(User.c.login == login)
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140
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141 # Execute the query and fetch the scalar result.
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142 result = connection.execute(query).scalar()
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143
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144 # Return the user_id as an integer if found, otherwise return None.
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145 return int(result) if result else None
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146
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147
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148 def get_projects_with_sample_count(connection, metadata, user_id):
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149 """
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150 Retrieve projects and their sample counts for a given user_id.
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151
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152 The query will return a pandas DataFrame with the columns:
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153 project_id : The id of the project.
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154 name : The name of the project.
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155 sample_count : The number of samples associated with the project.
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156
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157 :param connection: The database connection.
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158 :param metadata: The database metadata containing table definitions.
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159 :param user_id: The user_id to search for.
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160 :return: A pandas DataFrame with the projects and their sample counts.
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161 """
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162
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163 User = metadata.tables["ufz_user"]
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164 User_Project = metadata.tables["ufz_user_project"]
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165 Project = metadata.tables["project"]
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166 Sample = metadata.tables["sample"]
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167
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168 # Construct the query:
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169 # 1. Select project_id, name and the count of sample_id as sample_count.
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170 # 2. Join the tables ufz_user_project, ufz_user, project and sample.
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171 # - Join ufz_user_project with project on project_id.
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172 # - Join ufz_user with ufz_user_project on user_id.
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173 # - Join sample with project on project_id.
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174 # - Use an outer join to include projects without samples.
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175 # 3. Filter the results to only include the given user_id.
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176 # 4. Group the results by project_id and name.
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177
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178 query = (
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179 db.select(
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180 Project.c.project_id.label("Project ID"),
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181 Project.c.name.label("Project Name"),
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182 db.func.count(Sample.c.sample_id).label("Sample Count")
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183 )
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184 .join(User_Project, User_Project.c.project_id == Project.c.project_id)
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185 .join(User, User.c.user_id == User_Project.c.user_id)
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186 .join(Sample, Sample.c.project == Project.c.project_id, isouter=True)
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187 .where(User.c.user_id == user_id)
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188 .group_by(Project.c.project_id, Project.c.name)
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189 )
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190
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191 # Execute the query, fetch the results, and return the DataFrame.
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192 return pd.DataFrame(connection.execute(query).fetchall())
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193
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194
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195 def main():
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196
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197 # Parse command-line arguments
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198 args = get_arguments()
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199
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200 # Parse and check the specified command line arguments
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201 parse_check_args(args)
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202
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203 try:
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204 # Load credentials and create the database engine
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205 engine = get_engine(args.credentials_file)
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206
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207 # Reflect metadata and connect to the database
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208 metadata = db.MetaData()
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209 metadata.reflect(bind=engine, only=["ufz_user", "ufz_user_project", "project", "sample"])
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210
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211 with engine.connect() as conn:
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212 # Get user ID
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213 user_id = get_user_id(conn, metadata, args.login)
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214
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215 if not user_id:
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216 raise ValueError(
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217 "No Lambda-Miner user found with the login name \"{}\". "
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218 "Please find the description on how to register for the Lambda-Miner at "
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219 "https://lambda-miner-project.pages.ufz.de/lambda-miner-workflows/getting-started/."
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220 .format(args.login)
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221 )
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222
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223 # Get projects with sample counts
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224 projects = get_projects_with_sample_count(conn, metadata, user_id)
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225
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226 # Write projects as a CSV file to the specified output
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227 with open(args.output, "w") as f:
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228 f.write(projects.to_csv(index=False))
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229
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230 # Display the result
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231 if projects.empty:
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232 raise ValueError(
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233 "No projects found for the user \"{}\". "
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234 "Please create a project before going on."
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235 .format(args.login)
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236 )
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237 else:
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238 print(projects)
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239
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240 except FileNotFoundError:
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241 raise FileNotFoundError(f"Credentials file not found at \"{args.credentials_file}\".")
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242
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243 except db.exc.SQLAlchemyError as e:
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244 raise RuntimeError(f"Database error occurred: {e}")
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245
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246 except Exception as e:
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247 raise RuntimeError(f"An unexpected error occurred: {e}")
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248
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249
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250 if __name__ == "__main__":
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251 main()