Installation

We recommend creating a conda environment or venv for running the esg publisher.

Pip Install

Use the following command to install esgcet into a previously created conda environment:

conda activate esgf-pub
pip install esgcet
esgpublish --version #  Ensure you have upgraded to v5.3.2

All publisher requirements are installed via pip except for the CMOR tables (see below).

Installing esgcet via git

To install esgcet by cloning our github repository (useful if you want to modiy the software): first, you should ensure you have a suitable python in your environment, and then run:

git clone http://github.com/ESGF/esg-publisher.git
cd esg-publisher
cd src/python
pip install -e .  # You can modify the source in place
esgpublish --version  # Confirm that v5.3.2 has been installed

Now you will be able to call all commands in this package from any directory.

NOTE: if you are intending to publish CMIP6Plus or CMIP7 data, the publisher will perform several semantic relationship checks of the dataset properties to ensure . To enable this procedure, it is necessary to download CMOR tables before the publisher will successfully run, as those are required input for the checks.

Config File (esg.yaml)

Starting with v5.2.0 the ESGF Publisher uses a .yaml file for configuration. Download a copy of the default config file esg.yaml to the default directory,

or see below regarding migrating a previous config

wget https://raw.githubusercontent.com/ESGF/esg-publisher/refactor/src/python/esg.yaml
mkdir $HOME/.esg
cp esg.yaml $HOME/.esg

The config file will contain the following settings, most required settings are also available as command line arguments:

  • data_node

    • Required. This is the ESGF node (Fully-Qualified Domain Name) at which the data is stored that you are publishing. It will be concatenated with the dataset_id (instance_id) to form the full id for your dataset.

  • index_node

    • Required. This is the ESGF node (Fully-Qualified Domain Name) where your dataset will be published and indexed. You can then retrieve it or see related metadata by using the ESGF Search API at that index node.

  • cmor_path

    • Required for CMIP6. This is a full absolute path to a directory containing CMOR tables, used by the publisher to run PrePARE to verify the structure of CMIP6 data. Example: /usr/local/cmip6-cmor-tables/Tables This is either the cmor tables repo cloned from github or prepared using the esgfetctables tool part of esgf-prepare

  • autoc_path

    • Optional. This is the path for the autocurator executable. The default assumes that you have installed it via conda. If you have not installed it via conda, please replace with a file path to your installed binary. If set to none or removed, the publisher will default to scanning data using XArrary.

  • data_roots

    • Required. These are paths where you place your project data for publication, typically within mounted large storage systems, on the local server where running the publisher. Each entry maps the path to a logical subdirectory within a data url on the datanode. Please note two configurations (1) these may be different from the data node mounts –or– (2) may also appear in data node setup within esgf-docker configuations (Ansible playbooks or Helm charts) if the local publishing node uses the same mounts. Contact your node/site administrator for more info.

  • mountpoint_map

    • Optional. Must be in yaml dictionary format. Specifies an additonal mapping for the data root mounts that appear in the input mapfiles to the mounted data root on the host running the publisher, in the event mapfile generation occurred on a different host where the data resided at a different mountpoint.

    Changes specified “aliased” roots in mapfile to actual file roots like so: /source/path/in/mapfiles: “/actual/path/to/data”

  • cert

    • Optional. This is the full path to the certificate file used for publishing if publishing to a legacy esg-search site requiring authorization.

  • test

    • Optional. This can be set to True or False, and it will run the esgfpid service in test mode. Default assumes False. Override if you are not doing production publishing.

  • project

    • Optional. ESGF project to which your data belongs. Default will be parsed from the mapfile name.

  • non_netcdf

    • Optional. Enable or disable publication settings for non NetCDF data, default assumes False.

  • set_replica

    • Optional. Enable or disable replica publication settings, for sites that publish replica data. Default assumes False, or replica publication off (original data publication).

  • globus_uuid

    • Optional. Specify the UUID for your site Globus endpoint as configured in the Globus webapp. Default leaves out Globus URL from dataset metadata.

  • data_transfer_node

    • Optional. If you run the GridFTP service, set the hostname of that node, whether it the same as your data node or a sepearte Data Transfer Node for gsiftp urls in file records. Default of “none” will omit.

  • pid_creds

    • Settings and credentials for RabbitMQ server access for the PID sefvice, required for some projects (CMIP6, input4MIPs).

  • user_project_config

    • Optional. If using a self-defined project compatible with our generic publisher, put DRS and CONST_ATTR in a dictionary designated by project.

  • silent

    • Optional. Enable or disable silent mode, which suppresses all INFO logging messages. Errors and messages from sub-modules are not suppressed. Default is False, silent mode disabled.

  • verbose

    • Optional. Enable or disable verbose mode, which outputs additional DEBUG logging messages. Default is False, verbose mode disabled.

  • enable_archive

    • Optional. Enable the writeout of dataset/file record in xml files to a local file system. (see Archiving Info)

  • archive_location

    • Optional. (Required when enable_archive = True) Path on local file system to build directory tree and write xml files for record archive.

  • archive_depth

    • Optional. (Required when enable_archive = True) sets the directory depth of subdirectories to create/use in the xml archive. (see Archiving Info)

Fill out the necessary variables, and either leave or override the optional configurations. Example config settings can be found in the default esg.ini config file which will be created at $HOME/.esg/esg.yaml when you install esgcet. Note that while the cmor_path variable points to a directory, other filepaths must be complete, such as autoc_path and cert. This applies to the command line arguments for these as well. Additionally, a required setting if omitted can be satisfied via inclusion as ccommand line arguments.

If you have an old config file from the previous iteration of the publisher, you can use esgmigrate to migrate over those settings to a new config file which can be read by the current publisher. See that page for more info.

Project Configuration

You may define a custom project in several ways. First, using the user_project_config setting, specify an alternate DRS and constant attribute values (CONST_ATTR) for your project. DRS: is followed an array with the components. version is always the ultimate component of the dataset and should not be listed among the DRS components. If you wish to specify a custom set of Global Atributes you may do so using the .yaml section GA:

If your project desires to use the features of CMIP6 included extracted Global Attributes use the cmip6_clone config file property and assign to your custom project name within the user_project_config. The project name must be overridden using CONST_ATTR project setting (see example below). If you CMIP6 project wishes to register PIDs, you must assign a pid_prefix within config settings.

Example Config

The following contains example .yaml code and configures the primavera project as a user-defined cloned project:

cmip6_clone: primavera
cmor_path: /path/to/cmip6-cmor-tables/Tables
data_node: esgf-fake-test.llnl.gov
data_roots:
   /mounted/path/to/data: data_in_url
data_transfer_node: aimsdtn2.llnl.gov
force_prepare: 'false'
globus_uuid: 415a6320-e49c-11e5-9798-22000b9da45e
index_node: esgf-fedtest.llnl.gov
pid_creds:
   aims4.llnl.gov:
      password: password
      port: 7070
      priority: 1
      ssl_enabled: true
      user: esgf-publisher
      vhost: esgf-pid
project: none
set_replica: 'true'
silent: 'false'
skip_prepare: 'true'
test: 'true'
user_project_config:
   primavera:
      CONST_ATTR:
         project: primavera
      pid_prefix: '21.14100'
verbose: 'false'

Run Time Args

If you prefer to set your configuration to publish at runtime, the esgpublish command has several optional command line arguments which will override options set in the config file. For instance, if you use the --cmor-tables command line argument to set the path to the cmor tables directory, that will override anything written in the config file under cmor_path.

If you used the old (v4 or earlier) version of the publisher, you should note that the command line argument --config which points to your config file must be a complete path, not the directory as it was in the previous version. More details can be found in the esgpublish section. Some settings are not available on the command line and must be placed in the config file, such as the xml “archive” utility.