Database management configuration file

Every pipeline can accept a configuration file that contains user-specific information to enable the pipeline to be run automatically, including MySQL login credentials, NCBI credentials (for rapid retrieval of GenBank records), and server information and credentials (to retrieve data from, or upload data to, a server).

The configuration file is formatted to meet requirements for the configparser module. Below is an example of how it is structured with a brief description of each parameter:

[ncbi]                      # Settings for connecting to NCBI server
email=jane@acme.com         # Your email address
api_key=123456789           # Your NCBI api key
tool=DataRetrievalTool      # The name of your script

[mysql]                     # Settings for connecting to local MySQL
user=janedoe                # Your MySQL login username
password=random             # Your MySQL login password

[upload_server]             # Settings to upload file(s) to a server
host=abc.def.com            # Name of the host server to upload file(s)
dest=/path/to/folder/       # Server path to where the file(s) will be uploaded
user=janedoe                # Your server login username
password=random             # Your server login password

[download_server]           # Settings to download file(s) from a server
url=http://abc.def.com/     # URL hosting the file to download

Not every pipeline requires all information in the config file, so in general, individual sections or rows are optional. If a pipeline needs information not present in the config file, it will prompt the user for the requisite information. For NCBI, if you do not provide an email address or api key, your GenBank queries may be throttled or blocked (please refer to NCBI for more details). An example config file is available on the pdm_utils source code repository.