Qiita Client

Qiita (canonically pronounced cheetah) is an analysis environment for microbiome (and other "comparative -omics") datasets.

This package includes the Qiita Client utility library, a library to simplify the communication between the plugins and the Qiita server.

How to test this package?

In order to test the Qiita Client package, a local installation of Qiita should be running in test mode on the address https://localhost:8383, with the default test database created in Qiita's test suite. Also, if Qiita is running with the default server SSL certificate, you need to export the variable QIITA_ROOTCA_CERT in your environment, so the Qiita Client can perform secure connections against the Qiita server:

export QIITA_ROOT_CA=<QIITA_INSTALL_PATH>/qiita_core/support_files/ci_rootca.crt

Configure for cloud computing

In the default scenario, Qiita main and Qiita plugins are executed on the same machines, maybe spread across a Slurm or other grid compute cluster, but main and plugins have direct access to all files in BASE_DATA_DIR.

This can be different, if you set up Qiita within a cloud compute environment, where main and plugins do not share one file system. In this case, input- files must first be transferred from main to plugin, then plugin can do its processing and resulting files must be transferred back to main, once processing is finished. To achieve this, the qiita_client, as it is part of each plugin, provides the two functions for this file transfer fetch_file_from_central and push_file_to_central. According to self._plugincoupling, these functions operate on different "protocols"; as of 2025-08-29, either "filesystem" or "https". Switch to "https" for cloud environments, default is filesystem.

The plugin coupling protocoll can be set in three ways

1. default is always filesystem, i.e. _DEFAULT_PLUGIN_COUPLINGS This is to be downward compatible.
2. the plugin configuration can hold a section network with an option PLUGINCOUPLING. For old config files, this might not (yet) be the case. Therefore, we are double checking existance of this section and parameter here.
3. you can set the environment variable QIITA_PLUGINCOUPLING Precedence is 3, 2, 1, i.e. the environment variable overrides the other two ways.