The data dictionary provides the first level of validation for all data stored in and generated by BMS. Written in YAML, JSON schemas define all the individual entities (nodes) in the data model. Moreover, these schemas define all of the relationships (links) between the nodes. Finally, the schemas define the valid key-value pairs that can be used to describe the nodes.
Each branch within this repository holds the portion of the data dictionary representing a single BMS data domain. The root branch holds the central root of the dictionary that is common to all BMS data domains. The master branch holds the current merge of the dictionaries from all participating BMS data domains. The tagged releases are MAJOR.MINOR.PATCH releases of the master branch.
These links below will be automatically updated by a Github Action within a few minutes after creating a branch.
- Travis Build Status BRANCH master
- Dictionary Schema BRANCH master schema.json
- Dictionary Visualization BRANCH master dictionary-visualizer
The Data Model covers all of the nodes within the as well as the relationships between
the different types of nodes. All of the nodes in the data model are strongly typed and individually
defined for a specific data type. For example, submitted files can come in different forms, such as
aligned or unaligned reads; within the model we have two separately defined nodes for
Submitted Unaligned Reads and Submitted Aligned Reads. Doing such allows for faster querying of
the data model as well as providing a clear and concise representation of the data in the BPA.
Beyond node type, there are also a number of extensions used to further define the nodes within
the data model. Nodes are grouped up into categories that represent broad roles for the node such
as analysis or biospecimen. Additionally, nodes are defined within their Program or Project
and have descriptions of their use. All nodes also have a series of systemProperties; these
properties are those that will be automatically filled by the system unless otherwise defined by
the user. These basic properties define the node itself but still need to be placed into the model.
The model itself is represented as a graph. Within the schema are defined links; these links
point from child to parent with Program being the root of the graph. The links also contain a
backref that allows for a parent to point back to a child. Other features of the link include a
semantic label that describes the relationship between the two nodes, a multiplicity property
that describes the numeric relationship from the child to the parent, and a requirement property
to define whether a node must have that link. Taken all together the nodes and links create the
directed graph of the Data Model.
Each node contains a series of potential key-value pairs (properties) that can be used to
characterize the data they represent. Some properties are categorized as required or preferred.
If a submission lacks a required property, it cannot be accepted. Preferred properties can denote
two things: the property is being highlighted as it has become more desired by the community or
the property is being promoted to required. All properties not designated either required or
preferred are still sought by BPA, but submissions without them are allowed.
The properties have further validation through their entries. Legal values are defined in each
property. For the most part these are represented in the enum categories although some keys,
such as submitter_id, will allow any string value as a valid entry. Other numeric properties
can have maximum and minimum values to limit valid entries. For examples of what a valid entry
would look like, each node has a mock submission located in the examples/valid/ directory.
Configure continuous integration (test, build, deploy) of a Gen3 dictionary with Travis CI.
- Public dictionary repository (e.g. bioteam/dictionaryutils)
- Public S3 bucket (how-to)
- Travis CI account (sign up free for public repos)
- Development Environment (for Mac)
git clone https://github.com/bioteam/dictionaryutils.git
cd dictionaryutils
python setup.py developFrom within the AWS console, create an IAM policy e.g. travis-ci-policy granting access to only your public bucket.
{
"Version": "2012-10-17",
"Statement": [
{
"Sid": "VisualEditor0",
"Effect": "Allow",
"Action": "s3:ListBucket",
"Resource": "arn:aws:s3:::bms-gen3-dev"
},
{
"Sid": "VisualEditor1",
"Effect": "Allow",
"Action": "s3:*",
"Resource": "arn:aws:s3:::bms-gen3-dev/*"
}
]
}From within the AWS console, create an IAM user e.g. travis-ci with Programmatic access, adding the above inline policy.
access_key_id: <Travis_AWS_Access_Key_ID>
...
bucket: <your-public-s3-bucket>
...
upload-dir: <folder-within-s3-bucket>/$TRAVIS_BRANCH
...
repo: <your-git-org/your-public-repo>travis login --pro
# Username: <[email protected]>
# Password for <[email protected]>: ***************
travis encrypt <travis_aws_secret_access_key> --add deploy.secret_access_key --pro- Modify
gdcdictionary/schemas/*.yaml - Test (iterate until tests pass)
- Commit
- Tag
- Push
- Observe
- Verify
testdict
git commit -am "tagged release 1.0.0"
git tag -a 1.0.0
git push origin master --follow-tags
open https://travis-ci.com/github/bioteam/dictionaryutils
open https://bms-gen3-dev.s3.amazonaws.com/datadictionary/1.0.0/schema.jsonxcode-select --install/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"brew install pyenv
pyenv install 3.6.10
echo -e 'if command -v pyenv 1>/dev/null 2>&1; then\n eval "$(pyenv init -)"\nfi' >> ~/.zshrcbrew install travisInstall Docker (Mac)
echo -e '\ntestdict() { docker run --rm -v $(pwd):/dictionary quay.io/cdis/dictionaryutils:master; }\n' >> ~/.zshrctest